Finished podcast missing tracks on playback

OK, my brother's a digital audio engineer. I'm not.
I recorded students in class using (a very grindy-sounding) iPod 80G and a Griffin iTalk mic. Uneven, but it was the first time. I didn't even try to fool with taking out the whirring disk noise under the voices. I did try to raise the levels of the more mumbly kids. I pasted it all together, saved it, and uploaded it to (my) iTunes. When I played it back, though, the cuts I'd fooled with (not knowing what I was doing at all) were completely missing.
I read something after the fact about "clipping" doing this. Is this what happened? If so, knowing that I cranked up the track volume on the weak cuts to where the meters only infrequently hit the red zone, is there a better way to fix this audio?
Moreover, how can I rescue it from the .band project that seems to have all pieces intact and get all the audio to about the same level?
I had hoped to post this to our university server last night.
One more thing: sometimes when I try to open the project, it says a .wav file (one of the interview cuts) is missing. I don't know whether that was one of the ones I actually wound up using or not.
Any help welcome. I know a few basics of a/v production, but I'm primarily a writer and haven't worked an audio board per se since 1982.
MacBook Mac OS X (10.4.9) 2GHz Intel Core 2 Duo/1 GB 667 MHz DDR2 SDRAM/field recording with 80G video iPod/iTalk mic/anything

I read something after the fact about "clipping" doing this. Is this what happened?
Clipping is something completely different, it's a (nasty) form of distortion where peaks of a waveform are "clipped" off.
meters only infrequently hit the red zone
The "Red zone" is fine, the final led all the way to the right, and offset from the rest, is the clip indicator, you don't want that to light up.
it says a .wav file [...] is missing.
Although it shouldn't be necessary with what you were doing, the answer to this question is a good habit to get into:
http://www.bulletsandbones.com/GB/GBFAQ.html#saveasarchive 
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