When I look at the schematics of the reference boards, the simplest part of the circuit looks to be the crystal oscillator. There's a lot of complexity in there, and a lot of things that can go wrong.
Anyone interested in the details can start at this Wikipedia page, with the linked section hinting at problems:
http://en.wikipedia.org/wiki/Crystal_oscillator#Spurious_frequencies
Then check the excellent set of references on that page and head off to the IEEE:
http://www.ieee-uffc.org/frequency_control/teaching.asp
The listed Tutorial by John R Vig is excellent:
http://www.ieee-uffc.org/frequency_control/teaching/vig/vig3.ppt
http://www.am1.us/Local_Papers/U11625%20VIG-TUTORIAL.pdf
Also from Wikipedia is the following very old paper on oscillator design:
http://www.axtal.com/data/publ/ukw1979_e.pdf
It deals mainly with discrete transistor oscillator design. It also contains the following rather blunt observation on driving crystals with digital circuits (like we all do now):
"These oscillators are usually used where they are least suitable: in frequency and period counters, clocks and other measuring equipment."
But what could possibly go wrong? The following sentence on the above Wikipedia page caught my eye:
"A badly designed oscillator circuit may suddenly become oscillating on an overtone; in 1972, a train in Fremont, California crashed. An inappropriate value of the tank capacitor caused the crystal in a control board to be overdriven, jumping to an overtone, and causing the train to speed up instead of slowing down."
Tom (THE Random Poster)