As far as your particular problem...whether you're talking about the messages missing in a YAF system or a phpBB system my instinct is the same. Check the flags, are they marked deleted or is the system saving edits or something?
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When I post fp:mddubs in a topic, I'm leaving my footprint there so I can track it once I get into coding/supporting. (Yes I stole this off Mek 🙂, who stole this off Ederon 🙂 )
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...