I have this exact problem as well.  Every time the usb keyboard is
unplugged the delay rate is reset.  Touching the delay slider in the
keyboard preferences dialog.  Unfortunately adding xset to rc.local
isn't quite the right solution since that doesn't run when the keyboard
is plugged in.

In searching for answers I came across:
https://bugzilla.redhat.com/show_bug.cgi?id=499958

Apparently the fault is in gnome-settings-daemon and has been fixed in
gnome-settings-daemon-2.28.1-13 but that's not out for karmic.  However,
someone commented in that post that if you toggle the num lock key (a
quick double tap), the auto repeat settings are restored.  That's good
enough for me to live with.


** Bug watch added: Red Hat Bugzilla #499958
   https://bugzilla.redhat.com/show_bug.cgi?id=499958

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Keyboard repeat rate is often reset
https://bugs.launchpad.net/bugs/505029
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