The original firm ware on the GN3S v1 has a limitation of approximately 40 seconds. To overcome this the firmware needs to reprogrammed.
Download the new firmware.
The SoftOSGPS project has a valid firmware for download.
http://sourceforge.net/project/showfiles.php_group_id=91538_package_id=271229_release_id=645621
extract the file
browse to /osgps/gn3s-linux/gn3s-linux/bin
Figure out the vendor id and product id
make scan
unplug the device and do this again to determine the device that went missing, and this is your device.
modify your makefile to use this id.
In my case I changed the VID and PID to
VID=0×1781
PID=0×0b38
sudo make program
tell gn3s-full what sampler to use
./gn3s-full -s 60 -o data.bin
If you perform the following command again
make scan
you will now see that the sampler id has changed
bus 004 device 031 vendor id=0×16c0 product id=0×072f
unplugging and plugging back in the device will show the original firmware
bus 004 device 033 vendor id=0×1781 product id=0×0b38