Ergh... unfortunately, no, I haven't been able to fix them. What I ended up having to do was revert to a much older version--it only has the Battle Tower, but for the most part it works (a friend who's beta-testing says it's not recording streaks properly, and there were some hiccups adding some DP moves in, but there are only a few minor bugs in that version aside from that) and it was all I really needed. The Battle Tower is pretty much my whole game, though, as it's just to be a simple battle demonstration to show off some fakemon--I don't know if reverting is an option for you. I wish I'd been able to figure out what was up with the new versions, and I wish I could tell you more, but yeah... there were just so many problems and bugs that in the end I just had to throw up my hands and start over with an older kit. :/