First make sure that the rendering intent for gradients is set to 'No Color Correction'. You can do this in the default job setup for this printer in Production Manager or, sometimes, in the print and cut dialog for the job itself. Depending. However you have to do it, do it.
Next I'd give good odds that the gradient in question is set for RGB. In Flexi select the gradient, open the Fill/Stroke dialog and select CMYK. That would be the 4 dot icon instead of the 3 dot icon.
Then, just for good measure, in the Print/Cut dialog set the gradient algorithm to Super.
Do these steps and unless you have some other hideous thing going on, the gradient should print pretty much as you would expect.