While I haven't done that many CDLC's in the past, I've never had this problem, and I'm a bit lost. So long story short, these show up and work perfectly:

 

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

 

But e.g., these do not. Later on when green/orange repeats, they show up correctly again.

 

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

 

What am I doing wrong here? First I thought it was somehow about the sections, so I completely removed them but nothing. Doing non-DD.

Not entirely sure what you're talking about. When you say "show up and work perfectly", do you mean in game, i.e. that the 5-7-7 and 3-5-5 chords don't show up when you play the game, but the other stuff on the orange string does? If so, it's probably because they're marked as ghost notes (not sure how RS handles them, but anyway). I usually just handle ghost notes by converting them to normal notes via Ctrl+A -> Note (dropdown menu) -> Pro Guitar -> Remove Ghost.

 

(also, in terms of fretboard logic, it probably makes sense to move the 9-9-9 chords up a string to 2-4-4)

I agree it's probably because of the ghost notation (this causes the fret numbers to be shown in parentheses () ). These notes are not exported to the XML file when you save the project in EOF.

Yes, I meant in-game. And that was it, working fine now. Thanks for the help!