Pink, I'm with Mr. Wolsky here. I do my in and out, share, and I end up with everything within the range.
I have several Pixie Dust title generators over the Starfield background, as well as a scrolling text "credits" title with a video background. I've exported four seperate sections to iPad 720 for demo, as well as the full video to iPad 720 (4g) and 442 HQ (60g) formats with no missing items.
It worried me a bit the first time when the range only showed up on Primary Storyline, but after exporting and finding everything was still attached, I realized the range tool doesn't know what you are going to do with the result, so why would setting a range for output look any different than setting a range for any other purpose?
Koninda, I'm a small user, so just know a few things that get me by. Someone else will need to speak more expertly to address your questions. However, if I ran into the problem, my first question would be about what's happening with the audio conversion settings.
As a test (which solves nothing) I'd choose and export just audio. I have no idea where one goes about checking or changing what goes on with the audio.
Were the other 19 projects completed in FCPx? No matter how they were completed, there obvioiusly were no audio problems, but if you export your full project, is there still an audio problem? I know long long ago (like in 2002-3) with FCE there were possible audio popping difficulties when shooting lesser quality DV (16 bit ?) audio and up-stepping (to 32 bit?) once it was in FCE. Don't remember the details (or the proper terms), but perhaps something like that is happening. Tried to find the old discussion where Mr. Wolsky answered my question, but it is too ancient.
Can't possibly be an answer, but have you tried exporting a longer clip, like 1 min or 5 min just to see if the result is the same?