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.
We have a similar problem. A shared file with over 400 MB caused a poor server performance for the whole application. All users were affected. Got many bad featback from customers. The shared file was not broken. It was just very fragmented and there was a very large bookmarks of a user with alone about 170 MB.
Defrag the shared file did the job. I did not delete the 170 MB bookmark first. Now I did. Deleting this big one and defrag the whole thing shrunk down the filesize from 430 MB to 4.1 MB. No joke!!!
Application works fine for now. A shared file killed down the useability of an whole application. Could not believe it.