DoDMERB can be an obstacle to the application process, but the majority of it is about persistance.
It's far back now, but when I was applying my first time (back in 2000, lol), I was disqualified by DoDBERB. Then I ran out of time to provide a sufficient rebuttal by the time I was supposed to leave for inprocessing. (Less than a week before inprocessing, I had still not gotten a final answer!) When I applied the second time, I easily got a waiver.
My issues were due to dental malocclusion, by the way. In other words, my front teeth don't close all the way. They also noted my top four teeth in front do not have enamel, so they thought I had acid reflux of bulimia. However, the bottom line is that I did eventually get to USAFA. I just had to do a little more work than planned to get there!