The problem with clock displays like the radio is that the clock function is incidental to the main function. So the frequency of the electronic tuning fork Protagonist was talking about is determined by its main purpose, a frequency reference for the radio. That's going to be slightly "off" for a clock, since the math used to divide the frequency into seconds will be "good enough", but never precise.
It's an electronics design decision - instead of incorporating a separate frequency reference for the clock, they "mooch" an existing frequency in the radio. This saves a few pennies in manufacturing. The fact that everybody's clock is inaccurate by a similar amount is a pretty good indicator that this is the problem. It's designed to be a good radio, and a so-so clock.
If it was a dedicated clock it would be another issue. The frequency reference would then be mathematically accurate for converting directly into seconds.