I have a BIOSTAR G31D-M7 motherboard that i'm putting in an APEX case. The case has raised holes so you don't need to use standoffs (also it didn't come with any).
When I set the motherboard in, the screw in one of the corner holes won't reach the hole underneath. It seems that the motherboard is slightly warped, or the case is. Should I leave this screw out, or push it in a little bit and force it in?
You'll be just fine, just screw the board in there, be gentle though.
My Gigabyte GA-MA770-DS3 sat unused in the box for 2 years, under no less than 10, yes 10 heavy books. It was more than slightly warped. I took a huge risk and bought all components i needed to complete it once I could FINALLY afford to. And guess what, 7 months later it is still working flawlessly as a gaming rig.
The bottom line is, you can safely put a screw in the offending hole and gently/slowly tighten it down. Before doing so, I would recommend you loosen the screws nearest it, slightly, to help with any minor shifting that may take place. Take it slow and easy and you'll be fine.
I am a firm believer in securing all things as they were intended. Screws go where screws go and connectors are always firmly connected (like video cables, etc).