So I think I figured it out! (I'm pretty sure FCPX + Lion has issues with compressed audio formats, ESPECIALLY AAC and Apple Lossless!) There's a video of my findings below:
1. I tried doing exactly the same thing I was trying to do on my machine on a co-worker's Snow Leopard MBP, and it worked out fine (it was just importing an iPhone 4 .mov and exporting it in FCPX). The output file was pretty much the same as what came in.
2. I found out that only movies from my iPhone 4 were coming out all crazy in the audio, yet my Canon T2i files were fine. Both are H.264, yet the Canon T2i records audio as Linear PCM, while the iPhone 4 records audio as AAC.
3. So I got an idea to use screen flow to record a youtube video and record the computer's audio. Then I decided to export with different formats, both as HD NTSC standards and as web standards with H.264.
4. I found out that both NTSC and H.264 standards were perfectly fine, SO LONG AS THE AUDIO WAS LINEAR PCM (or uncompressed!).
5. I then exported the same clip (both times as H.264) and ONLY changed how the audio was rendered (either Linear PCM/Uncompressed or AAC) and VOILA, I got click and pop artifacts ONLY in the AAC version. The ones that were output as uncompressed audio were totally fine!
CONCLUSION:
Final Cut Pro X on OS X Lion has issues with compressed audio, MAINLY AAC and Apple Lossless! Anything that is Linear PCM/Uncompressed should be fine! For example, MPEG 4 AAC Enhanced Low Delay at 320K came out 95% OK, one or two clicks.
So if any of us are working with material where the audio came to us already as AAC (like an iPhone 4), then we have to rip the audio out somehow first (like through VLC for example) and import it separately as an uncompressed file.
Here's a youtube video showing exactly what I'm talking about:
http://www.youtube.com/watch?v=FDw4btShH0s