Collin, I just read your post, and I have been having the same problem. Exactly as you describe, and yours is the only post in months that has captured what I have been experiencing. I was wondering if you started noticing this problem at a point when you began working on a particular type of audio. Here is what I mean. I have a project where I got the video/audio from OLD vhs tapes. As a matter of fact, I copied the VHS tapes to DV tapes years ago, and just imported them to the computer in the last year. Here is the strange part. The camera I used to first digitize the vhs tapes and put them on DV had a 32kHz sound format I believe. Unfortunately, I don’t have that camera anymore. It was a Canon ZR10 I think. When I imported the DV tapes to my Mac, I am not sure, but I likely used the default capture settings I had which were for 48kHz. Then of course the sequence settings come into play. However, no matter how I set them, I get the same results. Here is one more variable. I did not seem to have a problem with the audio until I added background music. It was .mp3. However, if I remove these mp3 files from the timeline, the problem does not go away.
Does any of this sound familiar to you and have you had any luck fixing any of this?