Bob, for some reason all of my subscribed threads with new posts are not showing up in my usercp. It will show maybe one or two, when there actually have been new posts in many.
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Jade, when he reset the server or whatever, I had to go back and reselect my subscribing options.
I had the same problem as you - all the old threads from before the reset, I was still subscribed to, but not the new ones. I would check that out if I were you.