I had the same problem - my DoDMERB status was "Current Medical Status: Potential Pilot Qualified" and USAFA application page stated "Medical Status: Qualified."
I was pretty excited that I passed all medical requirements, but one day I decided to double check DoDMERB website and there was new information: "Current Medical Status: Pending Waiver Submission/Review", but USAFA website was still saying "Medical Status: Qualified". So I contacted USAFA to double check - and now I am DQ on both sites (D225).