As I've said, GSX makes a standard Simconnect call to check the standard engine variables, it doesn't have any knowledge of being in VR mode or not, or the loaded flight when doing it.
And not only that, the call is made periodically, each second, together with the check for the Parking Brakes, which means it can't be that GSX could have possibly skipped a check in these situations, because it's doing it constantly.
So, either Simconnect is really reporting the engines to be still running, or it just stopped calling GSX but, if this was the case, you should have seen an erratic behavior about the Parking brakes too, since the engine on/off status and the Parking brake are checked together in the same call. What happens if you release the brakes ? Does GSX detects that ?