I'm not sure if there's another forum thread for this problem specifically, but here it goes -
After installing the single-extruder arduino firmware, everything seemed to be working perfectly.
5 minutes later, I noticed that pressing Z's "Home" or "Home All" in Repetier started pulling z up, not down.
I reset the board, power cycled the printer, and even restarted Repetier to no avail.
Update: Z behaves as if the minimum value was 200 or so. As long as I make it go up a little first (Z+), I can then do Z- the same number of steps (i.e., if I click +2, I can then do -2, but then it stops, acting like position ~=200 is somehow the minimum stop position).