I'll just chime in, and say I have seen this on several of my songs as well. My songs are all less than 3 minutes, but seeing this in several of the songs from last year and now. I also changed to all different rates (128,160, 192 etc) all CBR, but no luck.
Wondering if folks didn't see it as much because they were trying to troubleshoot the wrong thing? Last year, I had been thinking there was something wrong with my FPP that was causing this.
This is difficult to resolve, since you have to "guess" where certain parts should be earlier than your normal timing marks, and always listen from the song from the beginning. Rather frustrating when you're trying to sequence a song with elements on the beat!