Huh. From the file I looked at the first name listed was the preferred one, and subsequent were alternates. So I theorized that it was overwriting the good data with bad. Here's the message I posted to FTDNA forums:
http://forums.familytreedna.com/showthread.php?p=354462#post...
http://forums.familytreedna.com/showthread.php?p=354462#post...