To troubleshoot this, I set up a new db in PT4. Then I found an original RTR Freeroll hand-history file where I had finished in the money. I compared this to a real money tournament file and saw that the freeroll was simply missing the buyin amount or "tag", so I copied my freerolls to another folder and made the following change with a freeware find\replace tool called TextCrawler:
PokerStars Hand #2776892893: Tournament #3773109, Hold'em No Limit (10/20) - 2013/06/06 20:36:09
PokerStars Hand #2776892893: Tournament #3773109, $0+$0 - Hold'em No Limit (10/20) - 2013/06/06 20:36:09
It changed 2600+ instances, then I was able to successfully import the histories and see the missing $400 appear in stats:
Now I will need to identify and purge the original hand histories from my main db, then import the updated histories and voila (I hope). The tourney graph should roughly match the old graph from OnlinePokerManager.
I'm really digging PT4 and can't thank CardsChat enough for selecting me as a gift winner in the holiday promotion.