I assume that your batch contained a command-line statement to reload the application with the parameter /r. I'm not sure but I believe it's the counter-part to the qmc-reloading feature performed through the qvb.exe. There none or at least lesser UI parts are included to perform the reload and therefore all actions which need a minimum of UI features are not executed respectively ignored.
But by using VBS for all parts of your task (opening, reload, export, whatever ...) you could bypass this restriction. Here some links which will be helpful to get this to work: