As GPOs are registrykeys most of the time, have a look at your isolations modes.
I don`t know exactly which reg key adobe requires for deactivating the settings, but have a look if you set "full" to the path where the setting is written via GPO.
Or maybe the setting is set within the project, so ne setting from the physical machine is "overwritten" in the virtual environment.
I`m really sure it`s an isolation problem.
We've spent a lot of time trying to solve this particular problem by ensuring that Group Policy can be delivered to ThinApp packages.
Here's how to do it:
You're right. That works great for any application which has "Policies" keys in the Registry. Office 2010 is a good example of that.
But I cannot name 3 other apps which use the Policies keys.
Indeed, MOST applications do not use the Policies keys: Acrobat, Firefox, Java, Lync, Autocad, FileZilla, FoxIT Reader, OpenOffice, Thunderbird, Shockwave.. and on and on and on. NONE of those use the Policies keys.
PolicyPak enables you to deliver the right settings directly into the ThinApp package -- dynamically -- regardless of where the application happens to store it's data (Registry, XML, INI, or other exotic data types.) And, if the application doesn't support "lockdown" PolicyPak will do it for you as you wish.
I would encourage every ThinApp administrator to at least check out the video here:
-Jeremy Moskowitz, Group Policy MVP