I suppose you are using AJAX to access the QVW, am I right?
As far as I know, AJAX doesn't refresh automatically the screen the same way as QV Desktop. The screen will only refresh when you interact with it, at least with a single click in a white area.
If you need the blink, you'll have to use IE Plugin.
* I imagine that in AJAX all the renderization is done at the server side and the server will push the HTML visualization to the client. So anytime you interact with the app, the client will make the request for a refreshed screen to the server and the server will return an updated HTML visualization. On the other side, the IE Plugin does the renderization at the client side, so it can automatically refresh the screen.