No, you cannot simply end task or end program trough the iGO sys command. This should be done with additional (mort) script. So first of all it all depends how did you install iGO application in the first place. Did you delete the original navigation and simply swap it with iGO? This is in most cases the best and the easiest solution. But If the original navigation sw is still present, than it's most probably related and connected to the device's main shell and this is the cause of your problem. But since I'm not familiar with this navigation device, at this point I can only rely on my gut

..and as I can see, you posted your problem on many different GPS forums across the globe so I don't really want to follow all suggestions and steps what you already did or you didn't try.. Good luck!