Only thing I can think of to try is get on the Korgforums PA4X forum, and ask other users who did the same upgrade if they had the same problem and know of a solution. A lot may depend on how you did your backing up before you did the upgrade, and how you restored your custom data.

Did you restore the keyboard to full factory resources first and THEN install your user data? Or did you simply install your data after you did the upgrade?

It has been quite a while since this update came out, I would think that most of the quirks of installation have been discovered and workarounds found for them. As long as you were conscientious in backing up properly before the update, I would hope you can get things back to the way they were.

Best of luck!