The color wiring on the motors that came with the Prusa i3 are, red, blue, green and black in that order from left to right.
I have other motors with blue, yellow, green and red from left to right.
There is no standards colors for stepper motors. its what ever the manufacture had laying about on the day
There are 4 pins on the reprap end, just check the first two are connected and the last two are connected and there is no connection from 1,2 to 3,4 with a multi meter.
If they are wrong those connectors are really easy to pop the wires out and swap them around should it be needed.
