Good afternoon,
Not sure exactly what you are referring to. My understanding is when you trigger a virtual stop (on/off) the MIDI messages transmitted are "MIDI note OFF/OFF" instead of ON or OFF). Or are you triggering a "Physical stop" (on your console) and it is sending OFF/OFF to Hauptwerk. If this is the case, then the program is with your console programming (not related to Hauptwerk)
For good measure power everything (computer, console, audio/MIDI/USB interface/hardware. and see if this clear the problem.
If what you are talking about is using a virtual switch to control some external components, then load Hauptwerk and the St-Anne orgam . Program one of the virtual stops the same way you programmed it (for another sample set I guess) an see if you can reproduce the problem. If so, then send me a diagnostic file (Help | Create a diagnostic.. ) and email it to support [at] hauptwerk.com . Specify which stop you programmed in St-Anne.
Feel free to provide additional information to clarify exactly your setup, what you're trying to do etc.
Hope that helps.