I have similar problems, and after researching Microsoft's support site, this appears to be a 'known issue.' with no fix at present. Try the workarounds:
(1) log out and back in. The problem with notification icons seems to happen after initial boot or restart.
(2) from task manager, kill explorer.exe, then restart the explorer.exe process right away.
I found my own method. For some odd reason, if I log in to my account too quickly, the tray icons do the nutty bit, but if I wait a couple of minutes, it works correctly!!
Unfortunately, this apparent Windows XP bug prevents me from using the TweakUI auto loggin feature that I so dearly want to use in order to recover from power outages and stuff.
Bob Dickow