Assuming that's not a bug, licenses are stored into PGO files, that in turn are stored in the Root Folder as specified in the QMC, System, Setup, QlikView Servers, Folders.
Are you moving the path to that folder in the process? Has that folder permissions for the user running the services or are you changing this user when you restart without checking?
Hope that helps.
Try creating a local server user and assign a license. If it let u,meaby u have communication problems with your active directory. That could cause the PGO corruption and won´t let u see the licenses.
Also chech your server name, change it for the IP address and give it a shot.