This doesn't make a lot of sense to me. If someone said that you are medically disqualified, they should tell you why. Vision, EKG, etc. If they aren't giving you the information, ask your POC at your base to call and find out why.
As far as waivers go, it really depends on what disqualified you. Sometimes if a blood test comes back abnormal, they will let you retest. The military is also less likely to grant someone a waiver for an initial flight physical than someone getting their annual. This isn't always the case...
I don't think anyone could even attempt to help you until you find out why you didn't qualify. Good luck...