That all depends on where you bake, I think 3dsmax, Blender, Xnormal doesn't need flips, but Maya does. Most baking programs have options to flip green on export, and if they don't you can set up an action in photoshop to flip green in case you've already exported lots of maps that aren't flipped.
Thanks for the replies you guys! Flipping the green did the trick, but does it consistently need its green channel flipped or only sometimes? Also I'm learning how to use 3dsmax, It has some annoying UI layout differences but it seems to have a better workflow somehow. Lots of useful modeling tools. I may try it out for a…