I have a GNS2000, and thought it faulty and had negotiated a return with the retailer when I thought to uninstall Skydemon then reinstall. It worked for me, and I now have a workflow which I use (in combination with my iPhone for Wx/NOTAMS and iPad for Skydemon) and it hasn't let me down. It does sound like you haven't got a connection with the GNS2000 though, as dublinpilot says.
I would ensure that one of your apps isn't running in the background when you start the other.