I'm not an expert, but if you're ok sitting upright, then you'd probably appear to look ok while lying on your back for the scans. It's when you invert and bend over that the problem arises. I'm not sure what would be out of alignment tho, but I'd guess your neck.
Wouldnt they be able to see all of that in a xray cat scan and mri? what could be out of alignment to cause a very bad headache
Have you considered seeing a chiropractor? You may have knocked something out of alignment in the accident that would only present when bending over.