Ok, well there is nothing that requires you to ground the motherboard screw holes. I can "breadboard" a motherboard without grounding its screw holes. So the problems you may be having with the mobo shouldn't have anything to do with the screw holes being grounded. If the "case" is wood, then either metal or plastic standoffs will provide the airspace under the board needed for cooling. They won't have any grounding effect. Anyway, based on what you are describing, there shouldn't be any problems with your board related to the mounting screws and screw holes.