The first problem is "Compact messages" operation caused all the messages to, hmm, be ultimately compacted, or in plain words deleted. Have restored it from the backup, so a few messages written after the last backup were lost. I apologize if it caused any problems for you. Some people may still find messages that
Next problem is forum theme -- basically you have to recreate it from scratch, haven't done that yet, still thinking of what layout will be more convenient.
Yet another problem we found only today is with private messaging, basically rendering it useless. The thing is, a new version of forum software introduced a separate limits on total size of private messages for admins and moderators. Strange enough, upgrade script did't care and just set the new values to zero! Tracked it down by reading the source code, fixed the limits, problem solved. Fortunately no one has seen it, except for the admins and moderators -- which is kinda funny.
Also, I fixed a bug in the forum code (well, technically not a bug but a bad interaction of old version of PHP vs. forum software) which prevented indexing of non-latin (i.e. cyrillic, i.e. russian) messages. So now it's possible for Russian-speaking users to use search.
Finally, I am still a bit unsure if the forum functions fine after the upgrade. So if you find any problems with forum, please let me know.