Z height wrong after z probing

I ran G29 after G28 XY, which seems to work fine. However, when I try to print something, the printer starts 2ish cm above the platform. I tried to change "#define Z_PROBE_OFFSET_FROM_EXTRUDER", but that doesn't seem to have any affect. Here is my start code:

G21 (set units to mm)
G90 (set positioning to absolute)
M82 (set extruder to absolute)

(**** begin homing ****)
G28 X
G28 Y F4000 (home XY axes)
G29 (bed level)
(**** end homing ****)

M109 S208 (Heat extruder)
; -- end of START GCODE -

I should also mention that I am using the nozzle as a probe (similar to the lulzbot). Once I get this sorted out, I will add some gcode to run the nozzle across a toothbrush head after heating to clean it.