Dear labrat,
Pulmonary function tests (PFTs) measure lung capacity and breathing function. If they also do a carbon dioxide exchange test it measures the degree to which your lung is exchanging oxygen. A CT scan on the other hand only shows the anatomic features of the lungs. If there is a problem on one it may or may not reflect on the other test.
I have not seen a case exactly like yours. This is really more in the expertise of a pulmonologist (lung specialist). If you are not already seeing one I would ask your doctor for a referral to a pulmonologist at the nearest major medical center or medical school.
I'm just really asking for help or even a second channce.