Just a note here for any users out there who may be running into issues distilling a PDF from a postscript file containing transparency,
I've dealt with this in the last week or so and it comes down to a simple text edit change of the Distiller setting file. Note, that as Matthias Guenther has mentioned in a few previous posts, anytime you print to postscript, your ps file will flatten transparency. So there should be no issues distilling a flattened ps file.
However, the benefit of Exporting to Postscript (i.e., a ps file instead of a PDF on Export to PDF) is that you maintain transparency in your PS file. It will not flatten, unless you export with a setting that instructs XPress to flatten the PS file.
OK, so here is the issue. Distiller won't distill transparent postscript files by default. BUT! You can change that. First, locate the setting you want to change (in my case it was the Press Quality setting). Believe it or not, these settings are actually text files. Make sure Acrobat Distiller is closed before you edit the settings.
Open the setting file in your text editor and look for the line that says "/AllowTransparency false". It should be at or very near the top of the setting file. Change the line to read "/AllowTransparency true". Save the file. Open Distiller and drop the transparent PS file on to Distiller (with that job option as your job option).
Barring any other problems with the PS file, Distiller should now happily distill your transparent PS file and you will have a transparent PDF as the end result.
Hope that helps anyone out there scratching their heads over this.