The first one is I am having to go in and out of Windowed Mode to get the vertical refresh to function properly
Try force-enabling vSync through AMD/nVidia control panel. If that doesn't work and it's seriously pissing you off, you may want to roll-back (or update) drivers with a clean install.
and the second, is that I'm wondering why Armor Mode recharges itself in MP.
You mean why it recharges while activated instead of slowly discharging like C2?
Because Armor is a million times stronger than it was in C2, now you cannot die until armor is fully drained and if you don't have armor up any AR can kill you with 3 bullets, Gauss/Bow with 1 shot, anywhere on the body, etc.
Flawed concepts to begin with = flawed design & mechanics built around said concepts. Auto Armor is a great example.