On "Hud Options" tab ("Configure -> Configure HUD") are you using a "Minimum Hands Required" value which prevents it from updating? Or a "Refresh rate" value with the same effect?
If not please see this about submitting a ticket (specifically "Pokertracker 3 log files"):
http://www.pokertracker.com/forums/viewtopic.php?f=45&t=20464You want to enable logging and play long enough to capture the problem you're encountering; be sure to include both "Pokertracker.log" and "PokertrackerHUD.log".
Mike