Hmm that config seems OK to me. The only difference with my config that might make a difference is the 'alpha_limit_enable' set to true on yours, mine doesn't have those lines (for alpha, beta and gamma). Try removing those lines (or set them to false).
Also you can try this: turn the machine on, and jog in Z in +1mm increments. Do your carriages go up or down? If they go down for +Z movements then you might have the issue below.
It's possible that you might have a combination of:
1) Wrong direction on motors, and
2) Endstops are not inverted.