Hope you're still following the forums. Some how I managed to get this working again....but not sure why it makes a difference...give it a try and let me know if it works for you as well.
Step 1: Go to DVRMSToolboxSettings - I have Comskip as perfered analyzer, and I click "Scan for commercials" at the bottom
Step 2: Click the FileWatcher tab - I make sure Output and Watched directories are in the \\Server\ etc.
Step 3: Click the Commercial Skip tab - Commercial Path is also \\Server\ etc.
Step 4: Click the Processing tab - Delay processing is set to FindCommercials and for Dection Profile is set to Find Commercials in DVR-MS, Click SAVE.
Step 5: In Start Menu -> DVRMSToolbox folder, click on DVRMSFilewatcher and make sure it shows up in your system tray.
That's all I did and now it's detecting commercials again on recorded tv shows on my windows home server. However, DVRMSFIleWatcher refuses to run for too long... (less than a day) and Vista will give me an error message saying that it has Stopped Working.