While I'm reporting it for the recent version, this bug is actually ancient:
In the "Command Shortcut" keyboard key selection dialog, the "Do not allow this key to be passed through" options is greyed out by default, and will only become available if a non-modifier key is pressed/selected.
That made it clear that modifier keys would always be passed through,(in VoiceAttack at least, some videogames for example do hook them), which is why I haven't reported it up until now.
However, the interface doesn't always reflect this; If the "Do not allow this key to be passed through" checkbox is checked while a non-modifier key is selected, it will not uncheck when that key is removed and only a modifier remains.
This persists after saving the profile and restarting VoiceAttack as well.