Onus :
Did you install the standoffs in your case? The motherboard is NOT screwed directly to the case, but on standoffs or raised bumps (not both) where the screwholes are. The single standoff I think you are describing is one that some cases have to assist with motherboard positioning.
There MUST be either a standoff or a raised bump at every mounting hole, and only where there is a mounting hole.
I am not sure, before I had a ATX board and all the screws went in just fine. But now I have a micro atx and the holes in the case is too far away from the mobo. Yes the only that that is holding in the mobo is the assist bump what shows where to position the mobo. The standoffs in the case matches the hole in the mobo, but the screws can't reach to secure tightly.
Maybe there is other parts I need to install to the case for micro atx? I don't know where the rest of the installation kit for the case is, it is a old case.