So I made my new basepose, looks fine in xsi. I added a keyframe for frame zero and one in xsi by root selecting bone_root and pressing the key icon in the bottom right. When I try to munge with the new basepose.msh I exported, nothing shows up in my side's folder. It works with a stock basepose.msh. Whats up with that?
Here is a screenshot
I noticed that my basepose had a lot fewer "lines" (Fcurves?) than the stock basepose. That must be the problem, but I don't know how to fix it.
EDIT: I solved it (i think). I branch selected the entire thing (dummyroot) and added keyframes at zero and one. It works ingame, even with the weird fcurves.