I would use some compressed air to blow out any dust and debris from the primary slot, just to make sure there isn't anything blocking full contact.
If the graphics card continues to work only in the secondary slot, you most likely have a bad mainboard. If it's in warranty, get an RMA. If not, time to buy a new one.
Note that there isn't much performance difference between a slot that runs at x16 and a slot that runs at x8. It sounds like you'd be losing a lot, but it's probably around 5-10%.