We're running into this now as well.
A few additional details on our situation: The QVW that's failing is one that reads several tables from a database and several Excel files and then stores each table to a QVD file. Reading from the database and storing QVDs works fine, it's the Excel files that are failing.
If I copy the folder the source XLSX documents are in and point my script paths to that folder, it works fine. Permissions are set up properly, the QlikView services are running as .\Administrator and the Administrator specifically has full permissions to the files and to the folder containing them.
We thought maybe someone else had the file open, but went into Computer Management and killed all open sessions and files and it still failed.
Any ideas for where to look next would be very much appreciated... Thanks in advance!