I have had the same problem too. Also recorded from a USB guitar interface, but not sure if that is relevant at this point. I have tried a few things to see if I could isolate the cause. Sometimes single shot recordings work right away, sometimes they don't. Somtimes combining clips cause Flextime to stop working. I have completely rebuit a project. Selected individual clips to play solo and exported the result. Took that output and placed it back into a new song and was able to stretch it for the most part. Which led me to believe that it was clip corruption causing the problem. However, while working to get some usable audio clips for a guitar solo, the flextime problems with garageband are starting to make it unusable. Right now I have two clips side by side in the song. I can stretch the timing anywhere in either of the clips. But if I join the clips, flextime no longer works in the joined region. It will only split the notes apart. So if either of those clips were corrupted, flextime would not work in one of them.
I have found ways to get flextime working normally again, sometimes taking up to an hour. Then five minutes later it breaks again. I'm getting really tired of having to recreate my songs to get flextime working again. It would be nice if someone would look into this problem sometime before the year is out.