This is still an issue for me. 
I'm running 8.04 (up to date) on a HP DV 1700 series laptop. When I use the GUI 
to swap the ctrl and caps keys, the key marked "caps lock" is still the only 
one that is triggering the LED. Actually, I ran the command 

xmodmap -e "clear lock" -e "add lock = Caps_Lock"

as suggested above, and that has fixed it for now (yet to restart).

On another computer running 9.10 (no way am I putting that on my laptop,
I'm sticking with what I *know* works), the problem does not occur.
(And, previously, running, I think it was 7.10 on my laptop, it didn't
occur either.)

If the xmodmap command sticks after restarting, I'll edit this.
Otherwise I'll try other suggestions in the thread and comment on them
too.

-- 
Caps lock LED changes state even when caps lock is mapped to ctrl
https://bugs.launchpad.net/bugs/173350
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