There's problem that could drive you crazy. Being able to sleep/wake and get it working again would mean that it can reset without shutdown or unplugging, so some kind of software solution should work. Unfortunately XPort doesn't reset real COM ports. I'll see if I can add those to the list though.
In my opinion, the GPS and COM port get out of sync. Baud rate, parity, or stop bits has changed on one but not the other. I'd be interested to know what happens if you hit Scan in XPort while it's happening. If it starts working at a different speed, that could tell us what's going on. Does anyone know what GPS is in there and how it connects to serial port and power?