What do you mean it deactivated it in desktop mode? I’m not sure what desktop mode means. You sounded liked you had a separate theme for your mobile devices called wpTouch, is this not the case?
My plugin is a responsive plugin not a device specific one so there isn’t such a notion as a “desktop mode” or “mobile mode” unfortunately.
I’m still not quite sure what you are trying to do as it’s quite vague so I’m kind of just guessing but you can still use the shortcode to only apply the menu on desktop devices with a simple piece of code like below: