This information is held in settings.ini. In QliKView 12, under Windows 10, this is stored in c:\users\<username>\appdata\roaming\qliktech\qlikview.
I have seen similar issues with sites that have implemented roaming profiles across virtual desktops. Normally this is a security issue with clients not being able to update certain folders in their profiles. I did have a site once that had replication issues between the various RDP and AD servers that did something similar.
I don't believe this is actually an issue with QlikView but rather the environment it is running in.
Hope this helps.