Yeah, if this is going on with the mod disabled it isn't mod related... except that it could be due to the fact that the box was opened and parts moved around. It is unlikely that the momentary switch triggered by the eject button has gone bad, a component like that is typically good for an insane amount of use. As Matt suggested check the eject PCB to make sure it hasn't been damaged. While you're in process of getting to it you will also have the opportunity to check out the wires that connect the PCB to the motherboard. Make sure they didn't get crimped up, cut or have any of the contacts pop out of the plugs.
-Whoopin