Can you post an example?
Not sure what "now sound like they are playing 8th note pedals through the sustains" means.
As in the other thread, I wonder if your resolution is 'course' (ie 120 default).
Doing the 'Fill' with a higher resolution may work better (smooth it out) if the Tempo change is sufficiently drastic.
Then again your system may be having trouble executing the regenerate .. hard to say without an example.

I do not work here, but the benefits are still awesome
Make your sound your own!