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The DO unmatch rate is about 30% for the last 5 years. Not all DO's get spots in the allopathic match. Having reviewed a large number of DO applications, I can tell you that DO Dean's letters are often difficult to interpret, training is variable between schools, and letters of refefrence are hard to evaluate. I tend to weight COMLEX/USMLE scores heavily (since these are at least standardized and I can interpret them). Hence, getting a spot as a DO depends heavily on your performance during medical school.
I agree that there is a large amount of variability between osteopathic medical schools. Some are established, affiliated with Universities and have a record of turning out high quality docs. Others are new branch campuses with nothing for PD's to work with. 1 DO program does not = another, more so than in the allo world. Sure, Harvard is better than xyz, but they all are established and well known.
The deans letter problem should certainly be correctable. I can't understand how LORs are hard to eval, I know students from my school (UNECOM) rotate at the same hospitals as Columbia, Tufts, UMass, UVM and Dartmouth students, thus receiving LORs from the same physicians (MDs and DOs). Maybe other DO programs are different. Boards are boards and I think the last point is very salient. It's not about the school or the letters behind your name, it's about the individual. Do well in classes, on rotations and on the boards, do some extracurriculars, rock your audition rotations and you will match. It's about putting in the effort and proving yourself.
Good luck to everyone scrambling!