Key settings are bugged
I have been trying to set "crouch" to Shift, but every time I go back "silent walk" is set to "mouse1" preventing me from firing.
Ok, can the quake team nuke whatever autosets keys to major commands?
I've never seen this bug before.
Have you tried using the console to set the keys instead of the escape menu? The only time I can remember having an issue is when I tried to reverse the mouse 1 and mouse 2 buttons so I could try playing left handed (fire/jump to jump/fire). This change wouldn't work using the escape menu, but it did work fine using the console.
The mouse button switch thing was a fairly recent test I did, perhaps this is a new bug.
Do you have an autoexec.cfg ? If so you need to type writeconfig autoexec after making changes.
If not it should stick.