For me, it always was a bit flakey at that point. When starting the RAM kernel, right after uploading it, the USB device will re-register. This point is probably not implemented very nice with regard to the Windows USB stack or the VM.
That said, I always had to "re-connect" the USB device to the VM manually at that point. The VM (though in my case VirtualBox) did not automatically lock into the new device.
You aren't running Linux underneath, aren't you? Because if so, I would encourage you to try k3flasher (there's a thread for it here). Hm, maybe I should finally provide compiled binaries for it. It has more informative status reporting and is maybe a bit more tolerant to timing stuff.