The custom I'm working on has sections where one guitar plays, but the other is silent for a good 30-45 seconds. I've set it with the "No guitar" section on EoF, but that section still shows up in the song when looking at the mastery overview above the chart. Am I not addressing the silent guitar properly, or did I miss a step?

Could you post a screen capture of the in-game mastery graph?

https://www.dropbox.com/s/v30fbojytugv9hn/noguitar1.jpg?dl=0

https://www.dropbox.com/s/qau8xfswvris7xu/noguitar2.jpg?dl=0

Those are the two areas in question. I have a similar problem on the bass chart but forgot to get the screenshot. From what I can tell, there shouldn't be that orange bar underneath (It's connected to the same one from the section before it), as that signals the continuation of that section. I've set it as a new 'noguitar' section, but no dice.

Far as I see it's completly normal 

Yeah, a noguitar section should display as a normal section (a segment of the yellow bar), but with no phrases (the purple towers) and it shouldn't be selectable in riff repeater. Can't guarantee that the last one is true from a screenshot, but it looks normal to me.

Ahh, alright. The yellow bar just didn't seem appropriate for whatever reason. Thanks for the clarification