Moosepilot-
What you are talking about happened to me. I had a current Class I flight physical, but was disqualified by DODMERB. I had to submit some additional paperwork, to include my flight physical. My problem was that I had two disqualifying surgeries, but had waivers for them. I saw an orthopedic surgeon, he wrote me a letter, and along with my waivers it was OK'd. No one anywhere in the process thought that I would not get qualified, but DODMERB just gets your stuff and spits out the simplest answer at first. It drove me nuts, to say the least, when I was getting a call on my cell phone about my disqualification minutes after landing a military aircraft. Having been in for 9 nine years, nothing that didn't surprise me.