Some DO schools don't consider SMPs? How to proceed?

I'm finishing up an SMP at an MD school (no linkage). Realizing that I am facing an uphill battle I have applied mostly DO (complete in mid-oct due to late mcat) and to my in-state MD schools. I am low SES and qualify for FAP if that matters. Got waitlisted/on hold for an II at a few schools. I feel that some schools are not aware that my graduate GPA is from a SMP and may be assuming it is a regular master's program (Which tend to have inflated GPAs from my understanding). Am I wrong... Some DO schools don't consider SMPs? How to proceed?
Source: Student Doctor Network - Category: Universities & Medical Training Authors: Tags: Pre-Medical - DO Source Type: forums