Although I am in no way an expert, I thought I'd write about a few things I have come across.
1. Slides
http://i.imgur.com/XJPPxQD.png
Example created in Guitar Pro 5
Shift slide
Legato slide
Unpitched slide out of a note (Slide Out Downwards)
Variation of (3)
Unpitched slide into a note (Slide In From Below)
1.1 Shift Slides and Legato Slides
In Guitar Pro, slides where the note is picked again after the slide are called shift slides.
http://i.imgur.com/31WPgzW.jpg
A lot of customs have shift slides where there should be legato slides.
http://i.imgur.com/QQPpi89.jpg
This can be fixed either by editing the tab in Guitar Pro and changing the slides into legato slides, or in EOF by giving the first note the Linknext status (select the note and press Shift+N).
http://i.imgur.com/Khi21rL.png
(The red arrow at the bottom after /7 means the note is linked to the next one)
A major problem is that TuxGuitar only has one kind of slide and as far as I know, examples (2) - (5) cannot be created in TuxGuitar.
http://i.imgur.com/NXpQuV5.png
The file created in Guitar Pro 5 opened in TuxGuitar.
1.2 Unpitched Slide Out of a Note
If you have a note like example (3) in your tabs, it will look weird in RS (although in this example, it doesn't look that bad).
http://i.imgur.com/ZOQjl51.jpg
Most likely what was meant was something like example (4). I think it's best to edit the note(s) in EOF, where you can use your ears and possibly the spectrogram to determine where the slide out starts.
http://i.imgur.com/HheYANq.png
http://i.imgur.com/65jBnTQ.jpg
1.3 Unpitched Slide into a Note
Rocksmith does not have this feature and example (5) will look like this in EOF and in the game if not edited:
http://i.imgur.com/EvwmUPI.png
http://i.imgur.com/eVYUQmd.jpg
Many customs have notes like these and it took me quite a while to realize what they actually meant. This particular example is supposed to be played by sliding from a fret lower than 8 into the 9th fret.
You will need to edit the note(s) in EOF and arbitrarily (depending on where your fretting hand is before the note) pick a note where the slide should start.
http://i.imgur.com/tnoeERF.png
2. Chord Sustains
2.1 Chords with too long sustains
http://i.imgur.com/AxCBpIP.jpg
This example picture makes the cause of the problem apparent: the chord that should have no sustain at all is followed by the same chord.
The fix is very simple. Apply the "crazy" status to the next chord.
http://i.imgur.com/Rdg17Fe.png
Select the chord an press "T".
http://i.imgur.com/Y1SJBUU.png
Notice how the 3D preview at the bottom changes.
2.2 Chords with too short sustains
http://i.imgur.com/Tx9pYEx.jpg
If your chords suddenly look like this, it means that the section or phrase (or FHP) changed in the middle of repeated chords.
You can fix it by applying the "crazy" status to the first chord in the section. Or in some cases, (re)move the section/phrase.
http://i.imgur.com/XvfQaL5.png
In this image it would mean marking the second A chord (at "verse 1") as "crazy".
If you know what you are doing and neither of the above fixes are suitable for some reason, you can use the tail sustain as a workaround (on a single chord with a long sustain) by marking the chord as 'sustain'.
3. Bends with Vibrato
http://i.imgur.com/AHZoKfW.png
Depending on the speed of the bend and the angle the camera happens to be in, notes like example (1) will look weird in RS. They will look like you are supposed to apply vibrato while bending the note.
A proper bent note with a vibrato should look something like this:
http://i.imgur.com/rg6yxRe.png
Tech view:
http://i.imgur.com/yBlsU6L.png
4. Unselectable Sections in Riff Repeater
EDIT: Looks like this is no longer an issue in the Remastered version. Customs should have DD in Remastered for the play counter to work anyway.
This has something to do with there not being a note on the beat where the section starts. One reason might be that the notes have not been snapped to grid (Song->Highlight non grid snapped notes).
You can fix this by resnapping the notes, assuming that your beats are in the correct places. Set the grid snap (Edit->Grid Snap) into a proper value. Select all notes (Ctrl+A) then select Note->Resnap (Ctrl+Shift+R).
What is the proper value? It depends on your custom. For example, if the smallest notes in it are 16th notes you can select 1/16 or 1/32 and resnap them all without worries. If your custom has triplets (and does not have notes smaller than 16th notes), I think it's safe to select 1/48 and resnap them all at once (somebody correct me if I'm wrong). If your custom has quintuplets or other irregular time divisions, you should not try to resnap all the notes at once.
If you cannot move the section so that it begins on a beat with a note, adding another phrase to the section (on a beat that has a note) should work, or you could try generating DD (See this thread).
5. Words in Lyrics Falling onto a New Line
EDIT: Apparently this has been fixed in the Remastered version.
A minor problem, but annoying for perfectionists. See this thread.
There doesn't seem to be a way to predict when it will happen. Most likely after a long note or a rest. You can try replacing part of the note's sustain with a "-", but this will affect the sustain of the note in the game. If it happens after a rest, you can try replacing the rest with a "-" .
A better fix is to append " -" (space followed by -) to the word at which the drop happens. In the picture below, it would mean that instead of replacing part of the sustain with a "-", keep the whole sustain and change the word to "shine -".
http://i.imgur.com/AVADtPE.png
Old workaround
http://i.imgur.com/R3sEsK5.pngNew workaround
6. Play Counter Not Working
In the Remastered version, the play counter will work only on customs that have dynamic difficulty. More specifically, a custom needs to have at least one phrase with at least two difficulty levels.
You can try replacing part of the note's sustain with a "-", but this will affect the sustain of the note in the game. If it happens after a rest, you can try replacing the rest with a "-" .My Tutorial | My Tools: DLC Builder | Custom Font Generator | DDC Improver | More