Microsoft recently released the iOS 9 Intune extension for System Center 2012 R2 Configuration Manager.
While I had updated my locally installed desktop consoles ok, the installation on our RDS server decided it didn't want to play ball.
Every time the console was opened, I received the prompt that a new extension was available and to install now or suffer having the console in read only mode.
However... each time I clicked yes to install, the console would close and then I would get a prompt saying the console was still open.
Checking task manager and logs etc. verified that no consoles were actually open, but when clicking retry, nothing appeared to happen and reopening the console would bring me back to the start off the loop.
Upon checking deeper, I could see the update process in task manager, which would go into a suspended state then resume then just quit.
A check of the event log revealed an error message with some form of .NET exception... oh...
I'll cut a long story short and after trying various things I finally tried running the installation process silently and it worked.
If you navigate to the ConfigMgr console installation folder (by default it's in C:\Program Files (x86)\Microsoft Configuration Manager\AdminConsole and run an elevated admin command prompt (or PowerShell) then navigate to the bin folder and then run:
This ran the installation smoothly with no errors and the console now opens fine with no prompts.
** Update 2nd Dec 2015 **
I've just had this same error after updating to SP1/2 CU2 and with the latest Conditional Access extensions, however the information above didn't work this time.
Looking at the log file, it recognised that the /Q parameter was being passed for a silent installation, but was complaining that no source had been specified.
Looking at the logs of a successfully updated device there was another parameter: SiteServerName=<<server name>>
So the new full command to run was:
AdminUI.ExtensionInstaller.exe /Q SiteServerName=serverFQDN