When I insert the card into its slot on the mobo I'm unable to press it all the way down. If I do, then the screw-hole doesn't line up properly with the hole on the computer case and I'm unable to lock the card in place.
What I've done is to seat the card only so far down as I need to in order for the brass strips to be completely hidden, but loose enough so that the hole for the screw lines up between the video card and the computer case.
Is this okay, or is it supposed to be seated all the way regardless or the screw placement?
The card should be fully seated regardless if it is not you will most probably get issues with it. Every card I have ever installed has made a faint or not so faint click when fully seated.
Obviously something is out of line. I have seen people put cards in and try to line them up with the wrong screw hole before. just offering as a possibility.
Can you post a picture of what it looks like ?