It's possible it has been fixed in the last couple years but for a while it was the case.

Were you -perhaps- using GNOME and the GNOME-provided GUIs to change monitor refresh rate? Given GNOME's history of legendarily user-hostile decisions made in the name of "simplicity", it would surprise me not even a little bit that the GNOME folks decided to pretend that the active monitor with the lowest refresh rate dictated the fastest you could drive any monitor.