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I'd also like to point out that some versions of Compiz seem to be more troublematic than some others. Last time I met a "nVidia+Compiz, missing window borders" -situation XGL didn't make any difference, but upgrading to the newest Compiz Fusion available fixed everything (except for the occational tricks and crashes of X/X apps, probably caused by nVidia driver).
The whole Compiz (Fusion) thing is at the moment so messy that if you have trouble with it, I advice that if you plan to switch/upgrade/install/remove any software regarding that thing, always first remove the software-to-be-dealt-with completely along with all possible configuration files (known as "purge" in some package management systems), then download and install the newest packages available (unless there is a good reason not to use the latest). None of those 3d desktop things is perfect, they all cause trouble of some kind, so you'll just have to try to find the best/least troublematic solution for now..
Also remember to restart your X server after doing some software changes relevant to it, and if you're dealing with graphics card drivers, it's a good idea to reboot the whole machine after that anyway. One of the rare cases where you want to make a reboot after a software upgrade.
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