I have PNGs that have a transparent background with a HEX Color set in the CSS for the background color (I set #CCCCCC - grey). When I PDF it it looks fine on the screen, but when it prints out, the background around the PNG prints slightly darker then the rest of the grey background.

I tried then to add the same color to the background of the PNG and saved it as a JPG, which looks the same on screen, but prints out darker as well.

I did a fix by making a 1px square with the grey color in it and assigning it to a repeat background image, with the transparent PNG on top. This now looks great on screen and prints out perfectly.

There is a bug when setting a background color in CSS, which would be great to have fixed as it would take up a lot less processing and faster. There may be a fix on this already but this is what I am running into.

Hmm, that's a tricky issue, as it may depend upon exactly how the PDF is interpreted by the printer, or the printer driver. Prince is only embedding the RGB colors and images as-is in the PDF, so it might not be easy for us to work around this. Do you have a simple test PDF file you could attach here for us to try?