CoreXy is only moving diagonally (6 replies)

So Im setting up my CoreXY printer using Marlin and Repetier Host, and no matter the plug configuration I use for the motors, the carriage only moves in diagonally. I have tried every configuration:

X                        Y
M1 forward          M2 forward          
M1 forward          M2 backward
M1 backward       M2 forward          
M1 backward       M2 backward
M2 forward          M1 forward          
M2 forward          M1 backward
M2 backward       M1 forward          
M2 backward       M1 backward

Is there something in the firmware I should try?

Also, one of my motors is mounted upside down because of how I have the printer designed. This may affect how the motors work, but I doubt it is a deal breaker.