This was happening to me too, and I found a solution.
1) Enable USB Debugging via settings > Applications > Development > USB Debugging
2) Clear Superuser Permissions via settings > Applications > Manage Applications (hit menu button and select filter, make sure "all" is selected). Find the Superuser app and select it. Click clear data.
3) If neither of those helped, try installing "Rom Manager from the Marketplace. Select the "Fix Permissions" option.
Note: Number 1 and 2 are what someone recommended for me to do, I don't know why number 1 should even matter, but I figured I would post it none the less. Number 3 is just a hunch of mine, but again, it can't hurt to try.