Ok, I'm beginning to think FlexTime has big problems when time signature changes are present (I've not seen this documented or acknowledged by anyone else, only the tempo change issue).
This section (again, left - FT off, right - FT on) does cross a time signature change, you can see the markers in the bottom 2 takes on the right (though they don't line up with the bar start). And rather than time compressing as it did to the take folder from the first post in this thread, it's time stretched both before _and_ after the time sig change.
This kind of failing is pushing me towards permanently using Melodyne instead of even having FlexTime as an option in my toolset. Grr
Late 2014 iMac 5K, 3.5 Ghz i5, 24GB memory - OS 10.14.6 - Logic 10.5.1 - Scarlett 8i6
Late 2012 MBP, 2.7 Ghz i7, 16GB memory - OS 10.14.6 - Logic 10.5.1