We are deploying our printers to Citrix Xenapp 6.5 servers running Server 2008 R2 using Group Policy Deployment instead of the Group Policy preferences at the moment. It's been a while since I originally tested the Group Policy Preferences. I believe we still get a prompt regarding trusting the print driver and have not tested further. We are also using PDFCreator Server v1.04 Build 328. I did configure a couple of group policies. One for Point and Click Printer deployment and one for allowing users to install device drivers for these classes:
I'm not sure I got the classes right and I've long since moved on to other problems without fully solving this one.. That's what I can recall, hope this helps.