I figured out what was wrong with all the topics that had posts scrambled. There were over 5100 posts that converted with invalid post date/times which was causing the problem. I was able to write some script to assign valid date/times to them within the proper post sequence which looks like it reordered them properly. There may be one or two wierd ones remaining (If the messed up post was the first one in the thread, it may still look wierd), but I think 99% of them are corrected now.
Moleculo
Moleculo