In my past experience, I have run across some similar issues as yours regarding tasks failing if a STORE to QVD is invoked in the load script., especially if the STORE commandand is called near the end of the load script. Something you may want to try would be to create a temporary auto-generated table immediately after the STOREcommand as the OS needs time to process file operations associated with the STORE command before moving on with the load script. An additional troubleshooting step you may implement would be to auto-generate a temporary table after the STORE command. This should allow enough time for the file operations to compete.
You could have the QVW developer include something similar to the below after the STORE command:
Load RecNo( ) as A, rand( ) as B autogenerate(100000);(Note: The parenthesis after autogenerate is allowed but not required.)