I was able to reproduce the problem and I did see Ctrl-S switches from one to the other.
The internal command "Mask Select" is disabled/enabled during a change dir among another operations and after being enabled it has priority over the custom command.
The priority is based on which command was the last one to be enabled or assigned.
The best solution would be to prevent the user from assigning a shortcut that's already assigned. However this is something we'll have to look into for future versions.
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