Thanks everyone for your help. Although 2.1-BETA did fix a couple issues I was having, it did not fix the issue with the serial ports. The pfsense menus seem to require you have a NMEA GPS (refclock 20) so if you want to use a different refclock you'll have to hack on /etc/inc/system.inc to generate the right stanzas in /var/etc/ntpd.conf. I stopped the ntpd service in the menus then jumped to the shell and ran ntpd by hand /usr/local/etc/ntpd -D3 -c /etc/ntpd.conf still no joy with the serial port. I have symlinked cuau0 to both /dev/oncore.serial.0 and /dev/oncore.pps.0 and also have my /etc/ntp.oncore.0 config in place which enables TRAIM and mode 1 (zero position mode). No Joy. /var/log/ntp/clockstats shows driver timeout on @@Cj (get config) command sent to the device same as before.
56382 82497.628 127.127.30.0 ONCORE[0]: ONCORE DRIVER – CONFIGURING
56382 82497.639 127.127.30.0 ONCORE[0]: state = ONCORE_NO_IDEA
56382 82497.641 127.127.30.0 ONCORE[0]: Input mode = 1
56382 82497.643 127.127.30.0 ONCORE[0]: Initializing timing to Assert.
56382 82497.645 127.127.30.0 ONCORE[0]: ONCORE: Can't open SHMEM file
56382 82497.647 127.127.30.0 ONCORE[0]: ONCORE: Can't open shmem
56382 82497.649 127.127.30.0 ONCORE[0]: state = ONCORE_CHECK_ID
56382 82498.514 127.127.30.0 ONCORE[0]: Oncore: Resend @@Cj
56382 82514.514 127.127.30.0 ONCORE[0]: Oncore: Resend @@Cj
56382 82530.514 127.127.30.0 ONCORE[0]: Oncore: Resend @@Cj
56382 82546.514 127.127.30.0 ONCORE[0]: Oncore: No response from @@Cj, shutting down driver
It looks like this is an issue with the motherboard/BIOS settings or somesuch at any rate I'm happy with 2.1-BETA and an busy building a new refclock based on a Raspberry Pi with the Adafruit 66 channel gps which will replace my old Motorola as my primary NTP server. I've got the Raspberry Pi ready to go with linux kernel pps and latest ntpd build just waiting on the Adafruit gps board.