Turning on Flex Mode changes timing of source audio

A multitrack project I'm working on requires some timing correction on one of the tracks. I turned on Flex Mode and set the track Flex menu to monophonic. The expected analysis of the track occurs, but then it appears as if it's already been subjected to Flex editing. Certain portions of the region show up as green, and others as orange, as if they've already been edited. Also, and this is the larger problem: the timing is all off! Turning on flex automatically extends the track a good 20 seconds in time, totally messing up the timing of the track relative to the others.
I am not that experienced using Flex, but I have certainly never run into this before.

Hi Fox,
Yes, this is definitely the cause of the offset of timing. I had to beat map the project in order to easily replace all the drums. The performance was unacceptable, so I used Audio to Score to convert the drum performance to MIDI, then loaded the MIDI into an EZ Drummer instrument. I was going bonkers guessing the timing corrections to improve the drums, so I beat mapped the bass/guitar tracks so I could edit the drums to a grid. It made a huge difference, but now I want to edit the bass track to correct a few timing issues, and that's where I ran into the offset flex audio. I think the most practical thing for me to do at this point is just edit by slicing regions, but now I've also run into an issue with the marquee tool, which I posted another thread about. I can't chop anything with the marquee tool! Augh! My only way to cut stuff is with the playhead slice or the scissor tool. AUGH!
Anyhoo, thanks for your help.
cheers,
Wally

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