Not sure if you're still grappling with this or not. I had a very similar issue. It was caused by a bad shared file. To fix it, our server team used a utility called, "Qlikview Power Tools". Not sure where to get it.
Either way, Qliktech's take on using this tool appears to be that you're on your own if it breaks anything.
So bear that in mind. For us however, it broke nothing but fixed the problem.