This might be just normal. I have a qvw where an external VBScript (which runs a query against an Easy Archive Server) is being executed from within the QV-Script. This VBScript takes ca 15 minutes to complete - during this time the qvw is "not responding". I get this warning several times during the daily execution of this script, but after the VBScript has finished, the QV-script continues to execute flawlessly. I have never found any mistake. So, in such cases there's no need to fix because nothing is broken. I would say with creation of QVD-files it's the same thing.
Actually, the reload always will work without any problem in that cases, but the warning only comes when reloaded by the (Standard) Publisher. You might have a "not responding" in the title bar of QlikView when reloading manually. All in all, I'd not worry about it.