Tom, with all due respect, I thought we all agreed that FCPX introduces clicks and pops when importing clips with compressed audio (like the iPhone 4's AAC audio). The manner in which FCPX handles the audio and converts it to an uncompressed format is what is causing all these issues. Do you have an iPhone 4? If you do, I challenge you to drop a video recorded on it through its native camera app (no third party apps where you can select to record audio as uncompressed by using frame rates lower than 30) and see if any of these problems appear. I have a video on YouTube that does exactly that, and this is the problem everyone's been having. What I clearly meant by my statement is that you can't natively use iPhone 4 footage (or any footage that records audio in a compressed format) because FCPX destroys the audio when it's imported. Drop any footage from a DSLR that records as uncompresed audio and you have zero issues.
So to be clear: it doesn't matter that all audio is converted to uncompressed audio when imported, it will introduce clicks and pops if the ORIGINAL audio was in a compressed format. If it was in an uncompressed format, you're all good to go. I've spent days trying every imagineable combination of codecs and what not to see if I can replicate the results and that is my conclusion.
Try this for example: on a project that you know for certain is working fine (i.e., no clicks and pops since all the audio was originally in an uncompressed format), export it as an MP4 file (which uses AAC for the audio). Now import that clip into a fresh timeline and tell me that it doesn't produce clicks and pops in Lion. Depending on the exact AAC codec you use, you get slightly better results, but the clicks and pops are always there.
If you cannot replicate these issues at all with compressed audio and you're running on Lion, I welcome you to share with us all your secret since apparently Apple themselves don't have a fix as of yet. Very frustrating indeed. ;(