In your original post you wrote
When using the physical stop, the light comes on and off as appropriate and the virtual stop follows along. So far so good.
Indeed - so far so good! But what is causing the lights to come on and off?
Do the physical lights also come on and off as appropriate when you click on the on-screen virtual stops, or is it only when you try to use pistons that they do not respond?
I initially had a similar issue with Classic Midi Works lighted stop tabs. i.e. the stop tabs would operate the virtual stops, but the physical lights did not echo the state of the on-screen stops (and Hauptwerk complained about MIDI feed back). For some unexplained reason they would not work with a Motu Microlite MIDI-to-USB interface and I was only able to get them working when I substituted a different MIDI interface.
Important - did you make sure to untick the option to toggle state of virtual stop?
Graham