I can confirm this bug.

I completely removed gnome-compiz-manager, removed .gnome-
compiz-manager in ~ and then .gnomerc.  I resintalled g-c-m, activated
"show tray icon" and it recreated .gnome-compiz-manager and .gnomerc
with that contents, so I must say, that it does write to .gnomerc.

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Gnome-compiz-manager thrusts itself into .gnomerc
https://bugs.launchpad.net/bugs/103246
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