There is a specific AD user group that you need to add the account that runs the Power Tools to. This group is not created automatically - so when you create it you need to ensure that it is syntactically spot on. Also be aware of which user account is being used to execute the EXE - if you are using Windows Scheduler or a CMD window it will not necessarily be the same user as the QlikView Distribution Service.
This text in the readme, gives the details:
Add the user that is executing the tool to the "QlikView Management API" Windows group. This group does not exist by default and must be created. Restart the computer or log out and back in again to let Windows update the groups.
Make sure also that you are running the correct version of the power tool for your QlikView server.
All is now running ok but this was a weird one.....
The groups and permissions had all been set up quite some time ago and every thing had been working ok until last Thursday. Simultaneously there have been some other weird [completely non QlikView] happening on our network.
I rechecked the groups and permissions you mentioned and all looked ok. Amongst doing many other things what seemed to do the trick was removing the AD Users from the "QlikView Management API" local server group.and then putting them back in, Plus a few other things I did that may or may not have been relevant.
As such it does not look like it was a QlikView issue at all, but permissioning issues external to QlikView.
The file qv-user-manager.exe.config was all set up ok, and I am pretty sure the issue caused by external authentication as since they are now sorted all is working with no changes to any QlikView / Power Tools config.