Be sure to check that all standoffs are located to match up with the motherboard mounting holes...and all mounting holes have a stand-off beneath them. To say it differently: remove only those standoffs that would be needed for an ATX board.
The standoffs are the spacers that screw into the bottom divider wall of the case and to which the motherboard is then screwed into through its mounting holes. Some cases come from the mfr. with no standoffs installed at all and some come with them all installed.
One of the more common build errors happens when people fail to remove an unused standoff, or don't put them all in. The motherboard then shorts out to either an unused standoff or the case bottom. Also, the force required to insert parts (GPU, memory DIMM's, 24pin power connector, the CPU heatsink, etc.) will bend the board quite a bit if it's not fully supported with the stand-offs which can crack a solder joint, again resulting in unreliable operation.