Are you only seeing it in the print only, or is it apparent on the screen as well?
If it's on the screen and the print, it's likely to be the software (or possibly your eyesight?)
If it's on the print only, then it's the print process
My money is on the software not fully grayscaling the image - especially if you're using the colour sliders to set different tones. Does the software have the facility to greyscale the image beforehand? Do you have any other software that can fully desaturate the colour once you've done the conversion? (i.e. Lightroom/Photoshop)
If it looks like it's the print process, does your print driver/dialogue have a black & white print mode? This usually desaturates the image. Printers can do weird things if you supply a B&W image and try using colour profiles to print it - especially if you only have one black ink cart.
The fact that it's only just started happening suggests a change somewhere. Have your print drivers or SEP3 been recently updated? If yes - check Google for complaints about the same thing.
THat's all I can think of.