I recently upgraded my GPU hardware to a GTX 690 (yay!). The GPU works fine, but it does not fit well into my mid-tower case:
Actually, what I meant by 'fits' is that the mounting brackets do not align with the holes on the case. As such I am only able to use my rig properly when it is laid sideways on the ground. i.e. the right side of the case (see picture) is on the ground. If my case is standing, then my GPU will not be properly set unto the pic-e slot since there's nothing holding the GPU from falling.
Question 1: Will leaving my pc rig in that position have a negative effect on airflow?
Question 2: How do I fix this?
It seems that there is a manufacturing flaw in the case, or your motherboard is not lined up properly. I would see where and if there are flexes in the case anywhere, and if you can't fix them RMA it. As for airflow I could see it having some negative effects as the hot air would stay at the now top side of the case a little more (but the mesh would radiate it) but I can't see it being more than a 3 or 4 degree difference at most.
That's a nice card you got there. I am guessing you are saying that the screws on the pci slots and the graphics card do not line up? Laying the pc on it's side is not ideal for airflow transfer. Post a picture so we can see how far off it is. I'm sure you could modify the case so it fits properly.