I'm clueless about what could possibly be creating this behavior, but when I try to home, for instance, the Z axis it first tries to move the X axis and than moves Z up instead of down just for a short burst and it stops. Something similar happens with all the other axis when trying to home.
The only thing I did was porting my configuration files from 1.0.2-2 to the new ones (line by line, not overwriting the whole file) and the only "new" option I touched was setting the board to RAMPS 13 instead of 14.
I have a homemade Prusa i3 and yes, 1.0.2-2 still works fine and as expected, this is not a hardware issue.
Any help would be appreciated.