I enjoy discussing science and philosophy with my co-workers. Here is a taste of the geeky conversations once held while employed at the local poly-silicon laboratory.
Interesting… then the problem is likely to be in the HeNe signal chain somewhere. Look at TP1 and TP2 for analog versions of the HeNe laser clock, and TP6 (or TP8?) for the digital version of that clock. It should look like a variable but mostly steady clocking sine wave or square wave.
Nothing beats the HeNe signal chain.