I can't help you with GPU Tracker as I have never used it. You might want to ask jedi for help in the tracker thread.
I would uninstall all your folding clients and start over. After you have uninstalled, make sure to clear out the following folders:
Windows Vista/Windows 7 GPU client:
C:\Users\(your user name)\AppData\Roaming\Folding@home-gpu
Windows Vista/Windows 7 CPU client:
C:\Users\(your user name)\AppData\Roaming\Folding@home-x86
Windows XP GPU client:
C:\Documents and Settings\(your user name)\Application Data\Folding@home-gpu
Windows XP CPU client:
C:\Documents and Settings\(your user name)\Application Data\Folding@home-x86
Windows 7/Vista 'SMP2' CPU Client:
C:\Program Files (x86)\Folding@Home Windows SMP Client V1.01
Windows XP 'SMP2' CPU Client:
C:\Program Files\Folding@Home Windows SMP Client V1.01
There are files in there that the folding clients use, and if they are corrupt then you will have problems. You need to have 'hidden files and folders' enabled to see those directories.
If you still have issues after that, use HFM using this guide:
How to set up HFM.NET and FahMon to monitor Folding@home progress. Now with videos.
And the post the exact errors you are seeing, copied and pasted from the log file shown in HFM.