Marlin Axis problem

Hello,
I have a Sumpod Aluminium with RAMPS 1.4 and Arduino Mega 2560. When I upload the test script everything works fine: LEDs flashing, axis moving back and forth, hotbed and hotend getting hot. When I install Marlin and I want to try manual movements, only the Z axis moves back and forth while all the others don't respond to commands sent and heater/hotbed don't get hot.
Where do you think there is the problem?

check your endstop status with M119 with the axis off all endstops, they should all read open. if not change const bool (AXIS)_MIN_ENDSTOP_INVERTING = TRUE; to false or from false to true or the max endstops

Exactly, they are all open.

Are you sending the commands thru an lcd or a UI like pronterface?

I am using pronterface on Win7 with the .exe file