Have you been closing the application after printing? I'm not sure exactly what causes it, but when I was doing prints out of Lightroom the other day on my Pro-1 and I closed lightroom. The exact moment I closed the program, the print (mid-line) developed the problem you describe. Reprinting and not closing the program fixed the issue completely.
My theory on the problem is that the ICC profile was dropped from processing when I closed lightroom. At the time I was printing on Canon Photo Pro Platinum paper. If your situation doesn't match mine exactly, the problem is still probably some information not getting to the printer from the application about the color space. Perhaps try printing from one of the packages that comes with the printer. Easy-PhotoPrint EX has been my prefered stand alone tool.
Also, if this is helpful and fixes the problem. Please let me know what about it you changed. I'm very curious as to what information dropped out to cause this problem when I was printing as well.