I'll throw my experience with this bug into the hat.  I just upgraded
from Gutsy, in which this feature worked correctly, to Hardy, in which
the bug appeared.  Hardy is currently up to date.

First, I reverted my Gnome keyboard preferences to the default.  I tried
Jay Finger's suggestion of placing MountainX's xmodmap instructions into
the ~/.xmodmaprc file and letting Gnome load that file.  However, while
this swapped the caps lock and left ctrl keys, like the Gnome keyboard
preferences option, it *failed* to correctly control the caps lock
light.

Then, I deleted the ~/.xmodmaprc file and tried Taylor Venable's
suggestion of altering the xorg.conf file, effectively making this a
global setting for all users.  When I next restarted X, at the gdm login
screen I verified that the physical left ctrl key was now both
activating caps lock and setting the caps lock light correctly, and that
the physical caps lock key was not.  So far so good...  I logged into
Gnome and opened a terminal.  Now, pressing the physical left ctrl key
toggles the caps lock light, but it still behaves as a ctrl key!
Likewise, the physical caps lock key toggles caps lock, but does not
alter the caps lock light!

It is important to note that at this time, there was no ~/.xmodmaprc
file, and the Gnome keyboard preferences were set to *default*.  Let me
repeat that the Gnome *default* settings were overriding the Xorg server
configuration settings! (Note: It is possible that some crufty setting
in gconf or something is causing this to happen, but short of blowing
away all of my dot files and directories and starting clean, I don't
know how to verify this one way or the other.)

My final attempt, that succeeded in working around the problem, is the
brilliant synthesis of the two previous solutions.  I used the xorg.conf
option *and* the ~/.xmodmaprc file.  The xorg.conf setting caused X to
behave correctly in gdm and caused X to show the correct caps lock light
status when I logged into Gnome, while the ~/.xmodmaprc file caused
Gnome to correctly swap the effects of the caps lock and left ctrl keys.

Obviously what is happening here is that a bug in the Xorg server is
hard-coding the configured caps lock key to the caps lock light.
However, it does seem that Gnome's settings are contradicting the
behavior of the configured keyboard options in xorg.conf and
substituting Gnome's idea of what the key map is.

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