Rainbow cube issue...

I decided to change to program on my cube, its been along time and a few computers later, i had a hell of a time getting the cube to talk to comp due to the driver for usb art not wanting to install, i finally got a good FTDI driver and im back in business only problem being as i load the programs to cube the RGB locations are off, when i load the CUBE 1 my blue is at 0,0,0 , green is at 3,0,3 , but red is at 0,3,3 instead of 0,3,0. This also flips the program where it lights up 1 row blue and 1 row green, each row is half blue half green. I recall someone telling me that something in the set up, i think it was in the rainbowdunio.h file, has to be flipped to fix this problem. the effects some of the examples but not all. Does anyone recall what i need to do?? Thank you !! Ty