Migration from OE and storage folder issue

I just bought a new computer and transferred everything via Windows Easy Transfer.  I'd researched ahead of time, so thought knew all the issues I'd have and thought I was good.  All my OE mail supposedly transferred into storage files.  I found them and all the folders were there, albeit in a different order.  I checked several, and except for realizing I may have to reorder some, everything looked good.  Went into a sub folder this morning and found an email with the correct subject line, but displaying an incorrect email.   It was an email from another subfolder.  Started checking more emails in more sub folders.  The same misplaced email is in message after message.  What happened to my email???  After spending the entire weekend setting everything up, I am so depressed.