Flex Time Creates Random Pops

Flex time is creating random pops after just minor correction of a monophonic bass line. The pops vary depending on where the playback starts in the file and they are recorded into merged or bounce in place audio. No plugs on the channel either.
Bob

I am getting that exact same problem too. A bass line that after using Flex time on, would randomly get clicks on it. I think it's doing it to the guitar lines too.
What seemed to work for me was changing the Flex time setting from Monophonic to Slicing. It kind of defeats the purpose of Flex time, but at least it sounds right again.
Hope Apple fixes this soon!

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