I've had this problem too. The weird thing is that it didn't actually appear to
change the setting-- i.e., I fired up gconf-editor and focus_mode was still set
to 'sloppy', which I could reliably change to 'click' or 'mouse' either manually
or through the Preferences > Window GUI and metacity does respond, albeit only
partially: specifically, it correctly changes the focus of the window it is
leaving, but it doesn't set the focus of the new window it is entering.

Let me be more specific:

1) metacity gets broken, somehow, while I have it set with a focus_mode of
'sloppy'. gconf-editor continues to report a value of 'sloppy'.
2) If I move the pointer from a focused window to either another window or the
desktop, the focus remains on the first window. I can change the focus by
clicking on the border or titlebar, so it appears to now be behaving as if it
were in click-to-focus mode.
3) I change focus_mode to 'mouse'. Now, when I move the pointer out of a focused
window, that window loses focus, but no new window gains focus when it is
entered. I can click to focus a new window.
4) If I change focus_mode back to 'sloppy', the behaviour reported in 2) is
repeated.
5) A restart of metacity (killall metacity) returns it to expected behaviour.

So to me it looks like the setting itself is not changed, but metacity at some
point doesn't behave properly focusing new windows. Alas, it's still very much a
Heisenbug for me. I can't reproduce the shifting into the broken state, but it
does happen.

I'm using the metacity in Fedora Core 1 (2.6.3-1). 

I believe I experienced the same problem yesterday, running CVS HEAD.  I didn't
investigate as far and I tend to switch between focus modes somewhat often
anyway, so I probably wouldn't notice as many symptoms (or at least not notice
the problem as soon).  So I'm not totally sure it's the same, but basically
metacity wasn't responding to my gconf changes to
/apps/metacity/general/focus_mode.  gconftool-2 reported that the changes were
occuring, though.  A killall to metacity set things back to normal and any
further gconf changes to the key worked just fine.  I'm not at all sure how to
duplicate though, since it seemed totally random when it occurred.

Also, it looks like this has been previously reported as bug 123267.  The
descriptions are just a little different, so they may be different bugs; but it
looks to me to be more likely that it's just different people trying to explain
a bug they haven't fully tracked down.

I noticed today a similar problem -- I couldn't change my theme at all.  No
change to the theme preferences had any effect, whether it be the gtk theme or
metacity theme.  After killing metacity, the changes to metacity were noticed,
but the GTK theme still wouldn't change.

Perhaps it has something to do with the fact that I was rebuilding my HEAD build
while running it, and I didn't log out/in after doing so.  For example, I was
able to fire up gconf-editor and the changes would be picked up, but that's
perhaps because it was started after the build and so had all the newer "stuff".

See also bug 154005.

I believe the bug Havoc was asking about was either bug 123366 (visual bell
modifies current focus window--looks unrelated), or bug 123267 (metacity seems
to forget settings--which I mentioned above).

No sense in having three bugs open about the same issue (or nearly the same two
issues; I'm not totally sure 123267 and 154005 are the same, but those two
definitely cover everything in this report)...

*** This bug has been marked as a duplicate of 123267 ***