I then overnight suddenly get dozens of messages marked as unread yet even though I have read these mere hours ago

Welcome to the read/unread bug. It started showing up around the time when the BBS switched from the perl to the php version of WWWthreads. It seems to only affect some users but no pattern has been found. The WWWthreads developer looked at the Empeg BBS for a few days but couldn't reproduce the bug, and that was quite a while ago. It seems that we are stuck with it.

Borislav