Thanks for your replies. It's a bummer that no one else is able to reproduce it, but I assume a lot of people haven't experienced this because we are doing music editing and remixing so we are importing audio from m4a or mp3. From your replies I played a little bit with exporting the tempo to the audio file and resetting the flex edits. While those things didn't solve the problem, I did see the behavior change. I'm thinking it has something to do with how logic is handling flex markers and/or the tempo of the audio file.
I'm able to reproduce this issue on every computer I have and very easily. If you drag an m4a in to your logic project. Set the tempo, then enable flex time on the track. Speed the song up by 10 BPM or more and then use scissors or marquee to split the audio. You may have to try a couple different edit points as sometimes it's fine, but depending on where you slice it, the end of the first half will get stretched out.
I'd be happy to make a video to show the problem if anyone can point me to info on how to do that.
Thanks,
Spencer