IIRC I didn't finding any easy way of making xmodmap settings persist over reboot, so I just took had a script that runs "xmodmap ~/.Xmodmap" run at startup.

(Of course then I switched to xfce on my laptop, which seems to run its own xmodmap command after its run startup scripts or something which overrides them, which is kinda annoying, haven't found a nice way to get around that).

I do expect a reboot to require somehow reloading my settings via xmodmap. More troubling is during an X session with Unity, my settings would be reverted, and I'd have to reload with xmodmap. Other desktop environments didn't have this issue. I really should have done my part and written a bug report.

Try putting your `xmodmap' command in `~/.xinitrc'. It gets read whenever the X server starts (`startx').

Thanks, but Xfce's startup applications list (which is just a frontend for ~/.config/autostart) is already executed after the X server starts, and after .xinitrc.

(Apologies if me saying 'runs at startup' was misleading -- obviously if I had tried to do it from a script that ran on boot, before X starts (rather than on session start) it could never have worked in the first place!).

Edit: now I've started thinking about it again, I've changed the autostart script to call another which sleeps for 10s before xmodmap, which seems to have fixed the problem.

I put it in my startup script, it runs every login.