Severe flex timing issues: song with varying tempo

I've been having a ton of trouble with flexing a drum track on a song with minor tempo changes (The song speeds up at the first chorus, and at the outro, so I programmed those into logic's tempolist so that the metronome would follow). Every time I turn on rhythmic, Logic speeds up the tracks (the wavefiles go green where the tempo change begins, and end much sooner than the files which are not being flexed). The only way I can get them to revert is to turn flex time off. It is driving me crazy as I only need to correct one minor thing, with a deadline approaching.
Incase it will help more, here is what I have done.
-Grouped drums together.
-clicked editing and phase locked audio
-turned on flex
-clicked slicing
-Logic analyzes the files
-suddenly everything is out of whack.
Is it something I'm doing wrong, or is it a bug in the system. Is there any way I get get Logic to analyze the files again? Any help is GREATLY appreciated.

I bounced and replaced all tracks, analyzed them again, and everything is working fine. Has anyone else experienced this bug?

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