Ive encountered it before: For a while I had two delays on my board, both powered with a non-isolated supply. The pulse in time with the LED was really noticeable with the other one, even on cleaner settings. The repeaters pulse was much quieter, but I could hear it if I listened for it- and it became more obvious with higher amp gain settings.
Switching to an isolated power supply fixed it for me. Ive not noticed it at all in the nearly two years since doing so (I've since removed the other delay, but am still using the repeater)