I'm running into an odd inconsistency and wondered if someone had an idea of what was going on/how to fix it (see the image below [image was edited so you can see the tech views of both piano rolls]).
To add to my confusion, I also made a 4-string arrangement whereby I copied the notes from this 6-string arrangement into the other guitar track, adjusted it for 4-strings and then copied that into PART_REAL_BASS. However, in-game in the 4-string path, both instances of this slide appear like 1, as opposed to just the earlier instance.

It might be worth mentioning that I placed everything in EOF by hand, no imports where used.

The produced xml even looks identical with the exception of time and sustain:

<note time="86.661" linkNext="1" accent="0" bend="0" fret="5" hammerOn="0" harmonic="0" hopo="0" ignore="0" leftHand="-1" mute="0" palmMute="0" pluck="-1" pullOff="0" slap="1" slideTo="-1" string="2" sustain="0.107" tremolo="0" harmonicPinch="0" pickDirection="0" rightHand="-1" slideUnpitchTo="-1" tap="0" vibrato="0" />
<note time="86.768" linkNext="0" accent="0" bend="0" fret="5" hammerOn="0" harmonic="0" hopo="0" ignore="0" leftHand="-1" mute="0" palmMute="0" pluck="-1" pullOff="0" slap="-1" slideTo="7" string="2" sustain="0.211" tremolo="0" harmonicPinch="0" pickDirection="0" rightHand="-1" slideUnpitchTo="-1" tap="0" vibrato="0" />
<note time="86.768" linkNext="0" accent="1" bend="0" fret="7" hammerOn="0" harmonic="0" hopo="0" ignore="0" leftHand="-1" mute="0" palmMute="0" pluck="1" pullOff="0" slap="-1" slideTo="9" string="4" sustain="0.211" tremolo="0" harmonicPinch="0" pickDirection="0" rightHand="-1" slideUnpitchTo="-1" tap="0" vibrato="0" />

<note time="306.304" linkNext="1" accent="0" bend="0" fret="5" hammerOn="0" harmonic="0" hopo="0" ignore="0" leftHand="-1" mute="0" palmMute="0" pluck="-1" pullOff="0" slap="1" slideTo="-1" string="2" sustain="0.107" tremolo="0" harmonicPinch="0" pickDirection="0" rightHand="-1" slideUnpitchTo="-1" tap="0" vibrato="0" />
<note time="306.411" linkNext="0" accent="0" bend="0" fret="5" hammerOn="0" harmonic="0" hopo="0" ignore="0" leftHand="-1" mute="0" palmMute="0" pluck="-1" pullOff="0" slap="-1" slideTo="7" string="2" sustain="0.214" tremolo="0" harmonicPinch="0" pickDirection="0" rightHand="-1" slideUnpitchTo="-1" tap="0" vibrato="0" />
<note time="306.411" linkNext="0" accent="1" bend="0" fret="7" hammerOn="0" harmonic="0" hopo="0" ignore="0" leftHand="-1" mute="0" palmMute="0" pluck="1" pullOff="0" slap="-1" slideTo="9" string="4" sustain="0.214" tremolo="0" harmonicPinch="0" pickDirection="0" rightHand="-1" slideUnpitchTo="-1" tap="0" vibrato="0" />

http://i.imgur.com/YUnfmce.png

The other difference is that the green notes in "2" are accented.  Accents do not work on all types of notes (for example you get gfx glitches if you accent a pre-bend).  I would expect the head to be missing as it has linknext status, the accent is probably causing a glitch that makes it appear.

 

Try turning the accents on.  Shortcut is Ctrl+Shift+A.

The other difference is that the green notes in "2" are accented.  Accents do not work on all types of notes (for example you get gfx glitches if you accent a pre-bend).

 

Try turning the accents off.  Shortcut is Ctrl+Shift+A.

This has been an issue since before I accented any of the notes and as you can see from the tech notes, the green notes that go into the slide are accented in both instances (I'd actually forgotten to accent the rest of the green notes in the first instance of this riff).

 

I tried removing the accents anyway, the instance at 1:26 still didn't work and the instance at 5:06 still worked, just as before.

 

It's not a huge problem that's going to stop me from releasing the cdlc when it's finished, it's only 1 or 2 notes and you can pretty much work out what you've got to do. It's just a bit weird and if someone does know what's going on and how to fix it, that would be great.

I changed my post.  I actually suggested turning the accents on...  I just got muddled up before.

 

If it's not the accents then I'm lost I'm afraid.  I would try turning specific notes accents' on off and testing.  If you say you are sure fair enough, it's not a problem I have encountered personally.

 

There are other methods of getting results - using crazy status and having the double stop which is linknext'd onto as two separate notes, so close together as the eye cannot tell but the game knows.

 

Linknext effectively turns note heads off.  The accent causes a "glitch" and forces it to draw a head anyway.

 

At least that's my theory...  I've been wrong before :D

I managed to fix this by selecting the notes that occur simultaneously, clicking on Note>Pro Guitar>Edit pro guitar Note and ticking the "split" checkbox. This normally 'splits' notes out of a chord box, displaying them as individual notes (I don't know if it alters how the game picks up the notes at all).

 

I guess either there was some sort of chord box interaction causing problems, or using the "split" feature bypasses whatever was causing the problem entirely, either way, it looks good now.