I'm certainly no expert but don't want you to think you are being ignored
here!

I have compiz on one system and it just works. It always comes back with the
same settings after every reboot. If you are having problems one thing you
might check is whether you have the right video card driver. That can make a
big difference if it is not the correct one and could cause going back to
the default or failsafe settings at every reboot.

There are some video cards that are very hard to work with in Linux and
there's not much one can do except find out the best choices and change your
hardware. Other than that I don't have any further ideas.