David,
Very strange. The code for handling NMEA output for the 700 is almost identical between 6.0.8 and 6.5.9. And we've been running this without fail in our test jig for several hours. Couple of questions: What is your OS version? (System Menu / Config / System...then read the number next to "OS"). Also, when you switch back to 6.0.8 are you swaping out the SD card? If so, there's a chance the settings are different - please verify your NMEA settings are the same in both versions. Finally, what do you have selected in the "Load Prolific Drivers at Startup" option? Can you try changing that setting and rebooting your device?
Thanks,
Walter