Flex Time degrades guitar tracks over time in Logic Pro

Why does Flex Time cause my guitar tracks to "degrade" over time? After recording I typically make timing edits in Flex polyphonic mode to small discrete regions. Each one sounds fine at first but after playing a session many times for additional recording and mixing, individual regions with those edits start to sound distorted. (FWIW, the wave forms don't look any different.) Turning off Flex for each affected region resolves the issue, but that means then either having to re-record those specific spots or living with my unreliable time.

As I keep working on a project more and more regions will end up with this problem. Sometimes I end up having to turn off Flex on up to 25%-30% of the guitar regions. The same issue can happen with vocals, but not nearly as often as with guitars (both acoustic and electric). I'm on Logic Pro 11.2.2.

Thanks for any insights.