I have been working on a project in InDesign with logos with transparent backgrounds sitting on colored backgrounds. In the InDesign file and the PDF (when I export it), the logo background color is consistent with the rest of the background, but when I print, the rectangle behind the logo comes out a slightly different color. Is there a way I can prevent this, either in my InDesign file or in my printer settings?
The conventional wisdom is to keep transparency live when you export, but if you are having problems with artifacts when outputting to an in-house, composite printer; the problem might be with the way the printer handles transparency flattening. In that case flattening the transparency when you export can solve the print problems.
See #7 in this thread: