This should be fixed now.

After some time passed, I realized that jdporter almost certainly had it correct. The timestamp changes when some process modifies a message, most likely when a message moves to a new folder. I saw the timestamp on some of my messages change when the sender's folder changed.

I found the one case of code that modifies private messages w/o forcing MySQL to preserve the existing timestamp and fixed it. This bug would have been triggered whenever anybody used Message Inbox to move messages into a new folder. In other words, timestamps on messages prior to today are rampantly wrong. Sorry.