Thanks but that is just a security update for an already installed Flash Player.
How do I install it in the first place so I can apply this update?
("Security Update for Internet Explorer Flash Player for Windows Server 2012 R2 (KB3065820)")
It's interesting that Microsoft is patching Flash and claiming it to be there product
("A security issue has been identified in a Microsoft software product that could affect your system")
I am not totally familiar with server 2012, you should have a control panel, correct, and a list of programs, did you look there to see if that would change anything.
Did you try and run this to see if it made a difference? Just a thought.
Also, that is how it is done in Windows 8.X ( bottom page )
Apparently Microsoft is including Flash in IE by default
In server 2012 / IE11 flash is installed by default by turning on Desktop Experience.