While it's important to have clean power when regulating precision timing, mains hum or switching noise doesn't really have the effect you're imagining - and the design of precision timesources and counters reflects that. You don't even need a linear supply to do a good job, you can just regulate a switcher's output fine enough, and if you took a switching supply that makes noise at a few kHz, you wouldn't see timing noise that reflected the new noise frequency. Also worth mentioning that when you're driving an OCXO, for example, the thermal mass/thermal time constant of the oven will be so long that it will be a low pass filter that blocks out anything over a few fractions of an Hertz in frequency - so even if the DC you were driving the OCXO's oven with had significant mains noise, that change in power applied to the heater would be smoothed out over so many seconds, the slower oven controller wouldn't even notice it.
What is your measurement method? If you're counting edges, this could be the normal cyclic variation of the way two frequencies align - think the moire effect or very-near-DC mixing products from two very similar frequencies.