Hello colors,
We tested this in our lab on a machine with the most recent firmware and we were not able to replicate the same issue that you are experiencing. We were not sure what version of Photoshop or Illustrator you are using, but we couldn't find the same problem. We also were not sure how exactly you created the transparent areas. Our first suggestion is to update the firmware on your machine. The link below should take you to the page on Xerox.com/support where the Drivers & Downloads are for the Phaser 8560. Scroll to the bottom and you'll find the latest Firmware version 4.9.4. Please try loading this firmware and post back to us and let us know if it resolved the issue.
http://www.support.xerox.com/support/phaser-8560mfp/downloads/enus.html?operatingSystem=win7