Ugh, give this a shot.
First, backup vars_config.cgi
Next, edit the file to show all fields as blank (ie, "")
Upload that file, overwriting vars_config.cgi (make sure you did that backup)
Go to the control panel, and you should be prompted for the paths again. Enter them.
Once you have the paths filled in, and have rebuilt everything, you need to open your backedup vars_config.cgi
Copy the Cookie Number from the old vars_config to the new one, which should have just been updated by the control panel. This way you don't need to have everyone log in again.
What you've now done is create a new cache directory, which should have all correct permissions, files, etc. You should now delete the old cache directory, and voila, your board should work
