While installing my new video card the thing barely lines up with the screw holes on my Antec 900 case. With a considerable amount of force I managed to get it lined up with one screw hole, with the motherboard flexing a few millimeters. I don't think ill be able to get it lined up with the second screw, but the first one is in pretty tight. Will I have to worry about the video card falling out of its slot if I only have it secured with a single screw?
Depending on how much it's flexing, the other end may be endanger of popping loose or making the slot loose from the motherboard.
It's likely an issue of the motherboard being shifted to far away from the back of the case. If you loosen the screws holding the motherboard in place (after you unplug everything of course) then slide the mother board closer towards the back of the case, then resecure it, you should have an easier time lining it up.
Yeah, I would take a look at the alignment of the motherboard with the standoffs underneath. The measurements on these things are all pretty standard, so you shouldn't need to be flexing the motherboard, or prying things so hard that something might break. Unscrew the motherboard screws (a magnetic screwdriver helps) and reposition the motherboard a little tighter and in alignment with the screw sockets underneath (called standoffs).
Also, I recommend pushing on the case to meet the screwhole on the video card, rather than pushing on the video card. For safety, if that makes sense.