It seems to takes hours after reading a thread for it to be marked as read. I know othe boards you can read a post, back arrow and hit refresh, and it's no longer marked unread. I've got 2 installs of ubb6 and both exhibit this same behavior.
UBB6 will not mark any posts read until you either logout, then log back in, or shut down all instances of the browser (and in some cases reboot). In UBB 6.1 there is an update posts indicator feature which will simplify the process.