If you haven't been here in a few weeks, take a look at this thread:
That should explain what happened to the unread post markers. The forum may have forgotten some or all of your previously unread threads/messages due to the 3-5 day delay in the upgrade.
It should work on a "going forward" basis, meaning unread threads from your first "post-upgrade" visit will be remembered and shown to you on your second+ "post-upgrade" visits. However, any "forgotten" unread markers on your first visit have been permanently forgotten. If the problem doesn't seem to have ironed itself out by your second visit, please let me know.
Sorry about that. It was a hassle for me too. I rely on those markers and ended up having to sift through a few weeks of stuff just to make sure I was up to date!