Thanks for the suggestion, but it didn't work. Ripple delete isn't working in either setting. My sequence is set to 48000 Hz and I have clips that have different audio sample rates (96, 48, 44)... but it doesn't seem to be linked to those because it happens randomly on the 48 files just as often as those that are 96 or 44.
I also tried moving the clips to Track 1 to see if that made a difference. It didn't.
I can't seem to find a pattern of when it works and when it doesn't.
Do you have any other suggestions?