URL's become URI's with Acrobat 9

A pdf that has been created in Acrobat 8 when viewed via IE with Acrobat 9 installed shows URL's as URI's and you are not able to click on them to follow the link.

Maybe you misunderstand. The standard output for the Adobe PDF printer it the PDF Port. That is indeed a print to a file (a PS file) and then Distiller is activated in the background to finish converting the file to a PDF. By print to file, I mean the print-to-file check box on the print screen. That will allow you to print to a PS file, though it may have an extension of PRN. You can then open that file in Distiller to complete the conversion. If that works, then your problem is likely that AcroTray is not running in the background.
AcroTray must be active for normal printer operation. When it fails you should still be able to print-to-file and then open the file in the Distiller to complete the process. That was my point and I am not sure that is what you have done. If it is, then I apologize for beating the point to death. The print-to-file is not the same as the PDF creation.

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