Are you using digital color separations? Proper calibration of that part, along with consistent methods in the printmaking process, should fix the issue.
I can recommend Calvin Grier's Gum Printing manual if you're curious about this process. It's theoretically in-depth without being overly complicated, and furthermore provides a plethora of hands-on/practical advice. He also has a digital calibrations guide, although I'd start with the gum printing one and then take it from there if you want to dig deeper.