Hi urrugby,
I don't know all of your specifics, so I can't comment on the specifics of your situation. Here is my general understanding though.
Assuming you haven't taken any of the basic sciences before (the usual situation for linkages) and you have a gpa above 3.4 and a good MCAT, than you should be able to get into an allopathic medical school if you apply broadly. Basically, you would be in the same situation as an undergrad with the same gpa. Linkages generally are looking for 3.6 or above, which is average. Plenty of people get into schools (allopathic and osteopathic) with below average gpa.
The linkages, I believe, reflect that the medical schools with these agreements with your postbac are familiar with your program and find it respectable. To do the undergrad analogy again, it would reflect the difference in going to schools with different pedigrees. That being said, the contribution of your program's pedigree pales in comparison to your actual gpa and MCAT. Medical schools will not likely take into account the pedigree of your program until after they culled applicants for gpa and MCAT, read the personal statements, and read the LORs. It is probably up there with your Extra-curriculars.
If I were in your shoes, I would be nervous if my gpa was below a 3.3. If that is your case, I would take more upper-level science classes and boost my gpa.