I don't think this is an actual bug. It looks like a mis-interpretation
of the feature... but there is probably room for some improvements.

The tool defines three profiles: "None", "Normal" and "Extra". "None"
turns Compiz off, and the two other options represent default "sets of
preferences".. so when the user selects one these two options, all
Compiz preferences are overwritten with the values corresponding to the
selected option.

When you install CCSM you get an extra option called "custom" which lets
you run CCSM...

The tool doesn't store which state it is in.. it simply looks at the
compiz preferences and checks their value.. if their value match the
"Normal" or "Extra" profile it marks that profile as being selected.. if
the values are different than the ones defined in these two profiles, it
marks "Custom" as being selected.

So here's what happens:

- You select "Normal" ---> all values are overwritten to reflect the "normal 
profile" (for instance desktop-size becomes 2)
- You then select "Custom" --> nothing happens... since you haven't actually 
made any changes in CCSM yet... 
- You close and re-open the tool... it looks at all the prefs.. and see that 
they're identical to the "Normal" profile so it shows "Normal" as being 
selected. 

You could leave "Normal" selected, close the tool and run CCSM.. then
change anything and see that the tool now shows "Custom".

It's not really a bug but it is a bit confusing. Ideally, the last
"custom" selection should be saved... so that even when you select
"Normal", although the prefs are overwritten you'd be able to simply
reselect "Custom" and get back to your previous preferences. Also, a
little flag could be used to remember the selection made in the tool...
in case "Normal" and "Custom" are actually the same... just in order not
to confuse the user.

Hope it helps. 
Clem.

-- 
[Gutsy] The Custom option in "Visual Effects" tab of Appearance Preferences 
don't persist
https://bugs.launchpad.net/bugs/151395
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