I know Im a baby in the sport, but Ive been there too. My first 6 jumps were rough. They were also during the winter, which Im sure didnt help any. But I was under a lot of stress at the time, and it basically made me bulimic (no i wasnt actually, I am a total foodie and very happy with my weight, I just couldnt keep food down). Anyways, I took a month or so off and got my health in order and finished AFF. I know military docs suck (I was dealing with Navy ones during that time), but some do know what theyre talking about. Its possible you just picked something up while you were deployed and need a bit more rest.
Edit to add: and by rough, Im referring to the vomicky/dizzy feeling under canopy.