Well I did find a base script doing a search on this forum for the conversion from phpBB 3 to YAF. I'm using a somewhat modified phpBB 2, so I'm using that script as my base and changing it as I go. The base script had Flags for ALL yaf_Message rows set to 22. From what I'm seeing, that is IsApproved, IsSmilies, and IsBBCode.
I can't find where the differences are between the messages that are displayed and the messages that aren't currently. This definitely seems related to the users. I just took a look at a topic. When I hover over that topic, I see the proper message listed by user x. The topic shows 9 replies. I click the topic and get 2 messages (but NOT the first message!). Both of the messages are from the same user. It seems only 1 of the users can be displayed...