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.
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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.