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.
This is basically a built in limit of X. The only exception is that monitors that support variable refresh rates may be able to offer this feature in multiple monitor configuration subject to software and hardware options.
I'm personally very dubious of the claim. This has basically never been supported because x treats all screens as one big screen unless you run multiple X screens which disallows moving Windows between screens which is a pretty big barrier to normal usage