raynebc

Then we should be OK for 99% of the time. I added the special save handling so if the bonus track is empty when you save, that track is omitted from the project and it can be opened in older EOF builds without trouble.
 
If you can make a Mac build for the next EOF hotfix, it would be great. With this major change, I want to allow for a little user testing and prepare to make a new "release candidate" to mark the occasion, although I'm basically still just using that term to reflect another "stable" beta release.

This is a bit of a complicated problem, but I have an idea of how to resolve it.

You're probably better off adding FHPs to the beginning position of notes. The FHPs that are generated automatically for your example looks like this:
http://i15.photobucket.com/albums/a354/raynebc/2%20anchors_zpso37283dm.jpg
And the resulting XML shows that the width on the second FHP was set to 5 to accommodate the Amin7 chord requiring that width:

<anchors count="2"> <anchor time="0.500" fret="4" width="4.000"/> <anchor time="1.000" fret="3" width="5.000"/> </anchors>One option to get the 4 fret width for the open chord is to place an additional FHP at the wide chord:http://i15.photobucket.com/albums/a354/raynebc/3%20anchors_zps0ot042fc.jpg
And this allows the open chord to get the normal width of 4 frets:

<anchors count="3"> <anchor time="0.500" fret="4" width="4.000"/> <anchor time="1.000" fret="3" width="4.000"/> <anchor time="1.500" fret="3" width="5.000"/> </anchors>You could also delete the FHP that was placed at the open chord and place it at the wide chord instead:http://i15.photobucket.com/albums/a354/raynebc/2%20anchors-2_zpsiblqglhq.jpg
This results in the first FHP covering the first chord and the open chord instead of having one for each:

<anchors count="2"> <anchor time="0.500" fret="4" width="4.000"/> <anchor time="1.500" fret="3" width="5.000"/> </anchors>

I'm guessing you set a grid snap value of 1/4 and the mouse is jumping from one beat position to the other.  That shouldn't prevent you from being able to select notes in between grid snap positions though.  Just in case, try changing the grid snap setting (the , or . keys, or use "Edit>Grid snap").

I think the issue is that chord's fingering defines the use of the index finger (numbered as 1) for both fret 5 and fret 8, which doesn't make sense. EOF doesn't check for this kind of conflict, but it warns that the fret hand position isn't at fret 8 when it sees the index finger is defined to be at that fret for this chord.

There are some tutorials around on this topic. To summarize, the process is usually to create a project, import a Guitar Pro file, enable the waveform graph (F5), enable the metronome (m) and move the beat markers (displayed as arrows --> ) to line up the metronome ticks that sound off during chart playback (spacebar) with the beat of the song (often the drummer). The instruments in the song will be reflected somewhat by the waveform graph, but the most noticeable effect will be that the snare drum will appear as regular spikes in the graph, and the beat lines generally line up with the beginning of these spikes. When the chart is "beat synced", you'll hear the metronome tick play at the same time as (or very close to) the drummer's snare drum, bass drum, etc. You can optionally enable claps © to allow sounds to play when notes are reached during playback to ensure they are placed correctly and claps occur where the instruments are heard in the song's audio.

The first likely possibility is you have placed the EOF program in a protected area of the file system, such as within "Program Files" or "Program Files (x86)", which would cause Windows (by default) to interfere and prevent files being written. The latest versions of EOF should warn about that location in particular, but it's also worth checking to see if eof_log.txt is being updated. If not, there is probably some sort of file permissions issue with the folder EOF is stored in. Moving the EOF folder to a different place is worth a try. If that doesn't fix it, let me know.

I'll ask the same things I asked in the EOF thread:
 
Have any previous EOF versions worked for you? What OS are you using? Can you send me the EOF log file?

Use the normal File>Load function to open it, but by default, that function doesn't display files that don't have an extension of "eof". You can do various things such as:
1. Type something like *.* or *.undo in the file name field of the "load song" dialog and hit enter (or click Open) and it will change which files are displayed.
2. Manually type in the name of the undo file when the dialog has browsed to EOF's temp folder and hit enter or click Open.
3. Rename the undo file to end in a .eof extension and then it should be displayed in the load song dialog.
 
After opening an undo state, you'll want to manually "save as" to ensure the project is saved into the correct location.

As was mentioned, in EOF the capo is treated as the nut position and fret numbering is relative to the capo. This seemed to be the most common practice with guitar tablature. Just something to keep in mind in case that's not the convention you're expecting.

If you go into File>Settings, do you get different results if you have different combinations of "Smooth playback" and "Disable Vsync" settings enabled?

In EOF when you have your project open, use "Song>File info" to verify where it really is. If the folder was actually marked as hidden, it's more likely that an error message would be displayed during save because Allegro (a library that EOF uses) doesn't seem to support working with hidden folders.

Go into "File>Preferences>Import/Export" and enable the option to "Save separate RS2 files".

Track>Pro Guitar>Set Tuning

For others encountering this problem, the solution is to enable RS export in EOF's import/export preferences. Running as administrator is not necessary unless EOF is located in a directory that is protected by Windows (ie. in one of the "Program Files" folders) or unless you're trying to save a project to the root of a drive (ie. at c:\ ).

I unpacked your file and imported the XML. 1015 notes and 47 tech notes were imported. Something to watch out for when importing a Rocksmith file is that the notes don't just import into the current track difficulty. This chart only has one difficulty, so they imported into the lowest difficulty number (0).

You would need to place time signature changes (ie. select the appropriate beat and use functions in the "Beat>Time Signature>" menu). The GP file should indicate where these occur. If you import a GP file, EOF will offer to automatically import the time signature changes unless the "Import/Export TS" preference is disabled or the project's tempo map is locked.

The pitched slide on that note is not valid.  It looks like you should re-define it by toggling the slide off, then toggling it back on and providing an end of slide position of 1.

Check out EOF's help menu. EOF comes with a manual that describes every single function, a guide to available keyboard shortcuts, and some lower level tutorials describing the basics of authoring within the program.

1.  Use "Track>Rocksmith>Tone change>List" to make sure your tone changes are listed and at correct times.  Whichever tone is the default will have "(D)" listed next to the name.  If none of them are listed as the defualt tone, use "Track>Rocksmith>Tone change>Names", select the appropriate tone and click the Default button.  It's also worth going to the Names dialog to make sure there are only the 3 tones you describe listed here.  If any of them were added with a typo or incorrect letter case, it ends up being exported as a different tone that has to be defined in the toolkit.
 
2.  You can turn selected notes into pinch harmonics with the "Note>Rocksmith>Toggle pinch harmonic" function (or use the SHIFT+H shortcut).  You can apply vibrato technique with "Note>Pro guitar>"Toggle vibrato" (or use the SHIFT+V shortcut).  You can set hammer on or pull off technique with functions in the Note>Hopo menu (or use the H or P shortcuts).  All of these techniques can also be set by selecting the note and using the "Note>Pro guitar>Edit pro guitar note" function (or use the N shortcut).

Sounds like your antivirus may be doing something like sandboxing EOF:
http://forums.comodo.com/install-setup-configuration-help-cis-b137.0/-t111787.0.html
 
Assuming you use Comodo, it should have a way to allow EOF to be run like a normal program.

You can import each of the tracks from the Guitar Pro file into separate tracks in EOF, or if you prefer you can go into File>Preferences and disable the "GP import replaces active track", allowing you to import each Guitar Pro track into a different difficulty in the same track in EOF.  Then after they're imported, you can select notes and copy/paste to combine them as appropriate.  Pasted notes are placed starting at the seek position, so using the Pg Up/Dn keys to seek to a specific beat before performing the paste is necessary.  If the paste needs to begin part-way into a note, you can use "Edit>Grid snap" to define an appropriate value (ie. 1/8 represents one half beat length), then you can seek that amount forward or backward using CTRL+SHIFT+Pg Up/Dn to line up the seek position nicely.
 
If the tablature being imported includes certain notations (especially bends), additional "tech notes" (kind of like a behind the scenes second set of notes that overlays the regular notes) may need to be copy/pasted.  You can find out if this is the case by pressing F4 to toggle the display of these notes on/off.  While this "tech view" is in effect, note operations are performed on this set of notes and the normal notes are just displayed in the background.

At 5:08 you have a note on fret 3 linknext into a note on fret 5.  This should probably be changed so that the note on fret 5 just uses the normal hammer on status.
 
At 6:09 there's a note with both bend and unpitched slide status.  I don't know if the game supports this.
 
This probably aren't part of the problem, but at 5:53 and 8:33, there are tech notes that aren't applied to anything, you may want to check to see if you intended for notes to be underneath them.
 
If resolving those doesn't fix the problem, maybe somebody else has an idea.  Otherwise you could try removing little bits of the chart content at a time (ie. the recent changes), documenting what changes so when the chart starts working, we'll have an idea of what caused the issue.

You can make a note a generic bend note by selecting it and using "Note>Pro guitar>Toggle bend", but this will just make the note bend 1/3 into the note's duration and the bend is held through the rest of the note.  If you want to be able to define more complex bends and indicate where bends begin and end within a note, you need to use tech notes.  Berneer has made a thorough tutorial on this:
http://customsforge.com/topic/890-tech-notes-tutorial-authoring-complex-bends-and-more/

You have to have Guitar Pro export it to Guitar Pro 5 (or older) format in order for EOF to be able to import it.