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.
(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.