I can confirm this behaviour on a thinkpad x40. the .Xmodmap is applied on boot, but plugging in a USB keyboard (in this case an IBM W20-06) the settings don't get applied to the hotplugged keyboard (but remain applied on the built-in keyboard).
Running xmodmap ~/.Xmodmap solves that issue, but only until suspend/resume or replugging the keyboard at which point i need to run the command again.
I can confirm this behaviour on a thinkpad x40. the .Xmodmap is applied on boot, but plugging in a USB keyboard (in this case an IBM W20-06) the settings don't get applied to the hotplugged keyboard (but remain applied on the built-in keyboard).
Running xmodmap ~/.Xmodmap solves that issue, but only until suspend/resume or replugging the keyboard at which point i need to run the command again.