I don't have a prusa i3, I have a homebuilt cartesian printer w/ dual Z axes.. I noticed a couple of differences between your config and mine.
Always_check_endstops - mine is 0
Babystep_Multiplicatior - mine is 1
Double_step_delay - mine is 0
Extruder_switch_XY_speed - I don't have that line I only have 1 extruder.
My printer homes nicely. I originally had Marlin (working) and switched to Repetier. I had to figure out the line syntax to copy my settings over from Marlin but it worked.