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In Ubuntu 13.04, all my nautilus bookmarks disappear after reboot, sometimes only some of them. I then revert to 12.04 as I cannot make my wireless card work properly in 13.04, but the problem persist.

I tried Nemo but to no avail.

If it help, I always format all my partitions whenever I install Ubuntu except one that I mounted as home directory.

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Create a new user and test there, if that works then is a problem with your local user. –  Braiam Jul 8 '13 at 13:38
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