Again, it all depends on your whole rationale for getting your Masters. For the vast majority of AF officers, their decision to get a Masters Degree is almost exclusively linked to their desire to progress in the ranks, and there is simply the added benefit of building their resume for their post-blue civilian carrer.
In this light, it makes absolutely no difference. All of the things you have mentioned are peripheral issues that mean absolutely zero.
As has been mentioned in the other thread on advanced degrees, most civilian firms that are going to hire you after the military are going to do so based on your military experience, unless you have a specific advanced degree from a specific range of schools.
In that case, it still makes absolutely no difference based on the pool of schools we're talking about.