I've encountered this with several different projects and I'm not sure where my error is.
I've edited a clip in Final Cut Pro 6, exported the audio as a WAV file. Then, importing the audio into Sound Soap to clean it up and resaving the file to be imported into Motion where I do finishing changes to the VIDEO ONLY.
For some reason, the audio imported in invents pops (speaker click or pop sounds) where there are no pops in the audio file. I've listened to it in Q-Time, Soundtrack Pro, etc... and no pops. But when on the timeline in Motion, there are pops. Any ideas?