Did you set the GPO for installing 10.0.1 to Upgrade or Uninstall Previous Version?
I deployed 10.0.0 with the Uninstall Previous Version option ticked. When the machine fired up, the message said it was uninstalling 9.4.whatever, then once that finished, said it was installing 10.0.0
[EDIT: You do lose any custom printing settings such as "print as image", if you do this - just something to be aware of]
For the change between 10.0.0 and 10.0.1, I selected the Upgrade option, and that correctly upgraded 10.0.0.
Hope this helps!
Message was edited by: GarethT42
OK, according to the documentation http://kb2.adobe.com/cps/837/cpsid_83709/attachments/Customization_Wizard.pdf I added the Property "REMOVE_PREVIOUS_READER" and set it to "YES" but the installation routine still doesnt seem to care