I'm having a problem with Nautilus in Ubuntu 10.10
When I open Nautilus as common user, it shows bookmarks and the bookmarks that point to smb windows shares work fine.

However, if I start Nautilus as root, it does not show bookmarks, and if I try to browse a smb share directly (by pressing Ctrl+L and inserting an address like smb://enrique@10.X.X.X/backups/) it doesn't work and gives me an error that it couldn't be found.

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This is expected behaviour. Your root user doesn't have a full set of gnome settings and it would not be a good idea to have it automatically connect to smb shares. In that direction, madness.

The root nautilus is only intended for use with your system files. It's not intended that you use it for connecting to network shares or opening files using applications. Both of which offer huge security problems.

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