calibre runs user mode code, i.e. it makes no kernel calls, therefore, it cannot freeze your entire computer. The worst that a bug in calibre can do is cause calibre itself to crash. If your entire computer is freezing, the bug lies elsewhere. As for your issues, just google: ubuntu 12.04 freezing and you will find this problem is affecting thousands of people most of whom dont run calibre.
For example:
https://bugs.launchpad.net/ubuntu/+s...rg/+bug/993187