I just upgraded the EndRun Technologies Tempus LX GPS receiver timing unit, and it seems to have fixed all the problems.  

Thanks to Steve for getting the info from EndRun.  There was indeed a bug in the firmware that was fixed with a firmware upgrade.

I upgraded both the system firmware and the firmware of the GPS subsystem:

Tempus LX GPS(root@Tempus:~)-> gntpversion 
Tempus LX GPS 6010-0044-000 v 5.70 - Wed Oct 1 04:28:34 UTC 2014
Tempus LX GPS(root@Tempus:~)-> gpsversion 
F/W 5.10 FPGA 0416
Tempus LX GPS(root@Tempus:~)->

After reboot the system is fully functional, displaying the correct time, and outputting the correct IRIG-B data, as confirmed by the VME timing unit.

I added a wiki page for the unit: https://wiki-40m.ligo.caltech.edu/NTP

Steve added this picture