I can't duplicate 1. For whatever reason, it sounds like its not able to connect to your GPS when starting up. This may be just because your GPS does not initialize when the startup routine begins, however, you should've gotten a message box saying this if this was the case. Run with -verbose and send me the log after having the problem. There should be couple lines saying PerformGPSStartup, followed by the failure of connecting to the COM port. The reason why it works after that is because if there is no connection to the GPS when entering the fullscreen navigation module, StreetDeck will always try to reconnect.
I'll have to look into 2 later.
3. Run with -verbose and send me the log when this happens.