We looked at the scripts shared to us privately by Sean and it seems that Reader was deployed via a patched AIP in his organization.
Please refer to MS documentation at https://msdn.microsoft.com/en-us/library/windows/desktop/bb204770(v=vs.85).aspx.
Under section “Avoid patching administrative installations.” Where it says:
“Many binary patches target the RTM image of the application and require a previous file version. The local instance of an application installed from an updated administrative installation may not work with other updates. Many binary patch applications can fail.”
Quarterly Patches for Adobe Reader XI target RTM and hence they won’t install on a machine where deployment has been done via patched AIP . You can also refer to the “Best Practices” section at https://www.adobe.com/devnet-docs/acrobatetk/tools/AdminGuide/aip.html where it says “If you previously deployed using an AIP, then you must apply the successive patches using an AIP”.
Due to the above cited reasons SCUP catalogs won’t be able to update these machines that have patched AIP deployments.
Our recommendation is that you deploy via SCCM and then you can patch it via SCUP. Or if there is a strong enough reason to go with AIP deployments then you must push all further patched through AIP only.