One thing I can think off that would cause colors to skew is gradient color mode. If you are using RGB colors to make up the gradient, set the gradient to RGB. If you are using a CMYK palette, make sure the gradient mode is set to CMYK. Flexi defaults to RGB.
I don't know if this is the specific issue you are having, but I'll throw it out there anyways.
Give us some more info on you're problem. Also, I assume you are using Flexi's RIP? Was the gradient also designed in Flexi?