Eythian: I am also having his problem with a hotpluggable USB keyboard.
This is a work laptop that I take to and from home; both locations have
a USB keyboard and every time I hotplug, I am required to unset and
reset (through System|Preferences|Keyboard|Layouts|Other Options...) my
ctrl/caps swap
I have this problem as well on Hardy B5, to which I upgraded this
morning 27 April from Gutsy. (My system has incrementally updated since
Dapper, so there *may* be cruft, but I've been pretty good about
revisiting my dotfiles.
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Caps lock LED changes state even when caps lock is mapped to ctrl
h