Still seems to be a problem
I just loaded up a file onto the iPad via iCloud and the colours were displayed incorrectly. The slides were all made from a PDF file. They still show correctly on the Mac. See my comparison where I have overlaid the original with the display from the iPad.
Just to check, I manually added boxes with the correct colours on Keynote for Mac and they showed the correct colour on the iPad. So it must be an issue relating to displaying PDF images from within Keynote for iPad.