Assuming you have restarted the QlikView Server computer after the updates, make sure that this computer does not have any other pending update, and that the .NET 4 Extended and Client Profiles are properly installed.
I'd recommend you to update to the most recent version of QlikView that is 11.20 SR1 release 11718 available to download in the Partner Portal or the Customer Portal.
As for the Windows updates, it might be some issues, but in any case they are not documented as far as I know. What I'd do first is to reinstall the current version of QlikView Server, just by going to the Control Panel and clicking on Repair, then rebooting the computer.
As for the update of QlikView Server, as they are in the same major version (11), the installer may ask to uninstall the previous version, but that should be all. All your documents, tasks, permissions and licenses will be there.
Anyway, as in any upgrade, make sure you have a recent full backup of the folder C:\ProgramData\QlikTech