Having trouble marking "as read"

I'm still having trouble marking threads "as read."  I use the UNREAD option for each forum.  Sometimes I will use the marking option on the sidebar, sometimes just read last message in thread.  Often, though not always, that message continues to show up the next time I go to that forum.  This has been going on ever since the major revision to the forum several weeks ago.  Either method used to work before these changes.