This is interesting in that the GPS stays up while using Seaclear but not of the Cap'n. An interestign thing to try would be a serial port listener application which will pump all the data form your port to a screen. If the GPS is still transmitting data when the Capn says you are sleeping you can lean towards the application as the problem. If indeed there is no data coming through the port then you can look into an OS/driver problem or a possible hardware problem with the garmin.
Give this a shot, Tucows Downloads - Serial Port Monitor 3.31 Shareware Software