Same thing here: KB3004394 removes/corrupted Windows Certificates so all windows system files are now found as unsigned. This is the reason why UAC comes into play and asks if you want to run an unknown program or file even when running the admin account,
but only for system files.
Seems this update corrupted the catalog folder/files within so windows now thinks all system files are unsigned.
As this update was specifically designed for this: December 2014 update for Windows Root Certificate Program in Windows and, must say, it has failed abjectly on one Win 7 64-bit SP1 with all other current updates successfully installed,
but not on another Win 7 64-bit SP1 system.
Uninstalling this update caused UAC to see all Windows system files as signed; but KB3004394 installed caused the UAC to warn all windows programs (mmc.exe, services.msc, etc.,) as/were unknown programs and caused the UAC to appear even in admin accounts.
Third-party programs were unaffected, and UAC operated normally.
Third-party firewall shows windows system files as unsigned when KB3004394 is installed, but as signed and verified when KB3004394 is removed.
Since this update is marked as Important, please provide a workaround or fix as soon as possible.
This update was marked as successfully installed after the system reboot on the problem system.