I think the reference is in Fire: It’s an offhand line about an ancient timekeeping system which the modern engineers mistakenly believe is calibrated to humanity’s first steps onto another celestial body.
As A Fire Upon the Deep is one of my favorite books (it's been a while since I've read it- my copy is currently on tour), I'd like to chime in and say I remember this reference, but I believe it's in A Deepness In the Sky, which goes more into Pham's backstory. It's definitely one of these two books though.
> Take the Traders’ method of timekeeping. The frame corrections were incredibly complex—and down at the very bottom of it was a little program that ran a counter. Second by second, the Qeng Ho counted from the instant that a human had first set foot on Old Earth’s moon. But if you looked at it still more closely. . .the starting instant was actually some hundred million seconds later, the 0-second of one of Humankind’s first computer operating systems.