DC's post is spot on. I have little to add....
It did worry me a little when you mentioned not being in an AMEDD unit or flex-training. I was under the impression that as a medical student/resident, you are given that designation and serve with a medical detachment?
Not necessarily, particularly as a resident. There are many vacant slots for docs in combat units in the Guard and in a lot of states, docs have congregated in med Det units, to the irritation of the line units. In some states, there has been a push to move docs out of med Det and into the combat units.
I guess my biggest concern, at least as stated above, was if you felt any particular programs saw your NG obligation as a negative and subsequently lowered your chances of matching in?
Some undoubtedly do. But you are unlikely to interview there as they'd screen your app out before you interview.
For programs that take a negative view on reservists, some may be small mindedness, but some may be from past residents not following DC's advice above and expecting the residencies to move heaven and earth for them. With a little planning and cooperation, you can get through without burning bridges. You can actually be an asset: many programs have VA associations and your military experience will help with some patients. Even on non-VA rotations, I've had vets ask specifically for someone with a military background and the department is happy to send them my way.
There is also a long history of docs getting their training in the military, and you'll be surprised how many you'll run across in academia. I have a hunch at the end of the day, it's likely about even between how many places your military association will help and how many it will hurt. I ended up matching at an extremely left leaning program and they were more curious than anything.
One final point, many programs, particularly academic ones, have "military leave." You may have to hunt to find it if you're the first reservist resident. Mine has 30 days/year, so my AT and Friday of three day drills is covered without eating into vacation time.
I'm very happy with my decision. I wasn't happy with what I saw of my options for military residency training. I also have a hunch that I wouldn't tolerate full-time Army life well. But I can tolerate it fine in short bursts and am happy to deploy during times of war, so the Reserve Corps worked out quite well,