photonboy :
Points:
Is it possible you are looking at a micro-ATX motherboard?
Regular motherboards have NINE mounts I believe and that should match EXACTLY to a normal ATX case. If you add a micro-ATX motherboard to an ATX case you likely have the BOTTOM THREE left over, but then they would be BELOW the motherboard and not in the way.
For some reason, manufacturers can't settle on 9/10 holes on an ATX or 6/7 holes on a reduced sized ATX...
There are a large variety of non-full-sized ATX boards that somehow are missing (usually) 1 hole near the PCI-E slots, so the board only requires (up to) 6 holes, like this board (I can't figure out what that extra hole on the memory side of the mobo corresponds to in standard ATX specifications, no cases I have seen features that middle hole...):
On that board, the PCI-E standoff mounting hole is missing. This board has it:
Some case manufacturers include a standoff in that position when you buy their cases, then typically that standoff in that position gets removed when the motherboard doesn't call for it.