I built and re-flashed my gumstix board with Steve Falco's modified source from http://docwiki.gumstix.org/NTP_Clock . I have exactly the same gumstix hardware (with the PPS line out to gpio) used in his project (sans the LCD and reset circuit).
 
My problem: Once I boot up the board and type ntpq - it does not run or return an error. What am I missing?
How do I add the PPS as a time server to the ntp client?

ntp was selected in the menuconfig before the kernel was compiled. root/usr/bin/ntpdate and root/usr/sbin/ntp are present.
I am able to cat the nmea output and pps (proc assert) from the command line.

Thanks,
Rahul