Hi Skywalker32,
I think Sabian is on the right track, well other than his nomenclature being incorrect. The way Acrobat/Reader works is the list of digital ID files are store in the registry like in the example above (except you'd be looking for 10.0 in the path and either Adobe Acrobat for your Acrobat users or Acrobat Reader for the Reader users).
So with that in mind, are you using a GPO to push the individual PFX files and are you using the Adobe Installation Wizard to customize the application (Acrobat or Reader) installs? I'm just trying to get a handle on what's in play here. Also, I thought that maybe the digital ID file location could be set as a lockable preference in the HKLM portion of the registry, but they can't so if that's what you are trying to do via the installation wizard that could be a problem (not that I think you are, I'm just taking a shot in the dark here).
Thanks,
Steve