When I first built my Prusa i3 I got lucky enough to find someone who had uploaded a pre-configured copy of the repetier firmware. I uploaded his firmware to my printer and it just worked, like magic.
Unfortunately I ran into a hickup when helping my son with his arduino based RC car. I accidentally uploaded his arduino program to my printer. And when I looked for the pre-configured firmware again I was unable to find it.
So, I downloaded the latest and greatest repetier firmware with all default parameters, uploaded it, and kept my fingers crossed. After about a week of experimentation I realized that my end stops were the only thing not functioning correctly, they seemed to be placed on the wrong side of the axis for some reason.
Another week of playing with settings and no success I finally ran across this post. All this time I had been focused on my Endstop configuration, it had never occurred to me that was not where the problem lay.
I jumped down to the XYZ movements area, located :
#define INVERT_X_DIR 0
#define INVERT_Y_DIR 0
#define INVERT_Z_DIR 0
and changed them to:
#define INVERT_X_DIR 1
#define INVERT_Y_DIR 1
#define INVERT_Z_DIR 1
And I was back in business, everything was working they way it was before. This time I backed up my configuration in case this happens again.