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The same logic applies to X.org as applies to the kernel, because calibre (and all other X clients) talk to the X server via a protocol, or in other words, calibre executes no code whatsoever in the X server, and has no access whatsoever to its memory (calibre does not use hardware acceleration). X server freezes are bugs in the X server (or more likely the graphics drivers or the compositor).
There is no better bug report to be had, this is not a problem that can be fixed at the level of calibre. If I were you, I'd just switch to a sane window manager till the bugs are ironed out of gnome 3/unity/whatever.
If you want to help track down the bugs in X/gnome3/unity, you'll need to ask in one of their forums.
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