Is this brand new? What was it that led you to pull the cooler?
It sounds like a physical failure from the pressure of mounting. You never want to run without a cooler though. I would suggest loosen all of the motherboard mounting screws slightly (make sure power has been off and discharged and the power line is not connected), and then snug them back down. The idea is to let the motherboard choose the least stressed position. If any screw is still tight prior to tightening them back down it won't help. Do keep in mind you don't need to use a lot of force, typically about 4 inch-pounds. Don't tighten any one mounting point completely, go around snugging a bit more on each mount point until you get a reasonable torque. You don't have to...