Well, I have now tried your suggestions, it seems that I still loose between 30 and 45 minutes of data. I don't know if this is really data lost or just time stamp issues. I have my LED flashing on the AO channel, it doesn't stop running even when the time server is rebooted. Also added a loop counter, seems that the counter is off by 6 minutes instead of 5 when I check the counts. (I am trying a 5 minute ave.)
I am almost out of ideas. The system is autonomous except for the time server. I can let the system run for days, if I don't reboot the time server, and it will be fine.
-- Confused and frustrated!