Safari bookmarks keep disappearing
If the bookmarks are not saving this may be a permissions issue. 

Safari stores its bookmarks in ~/Library/Safari/Bookmarks.plist

If this file cannot be updated (i.e. if permissions are wrong), then the bookmarks won't be saved.

Check the datestamp on this file. It should be updated every time you add a bookmark. If it isn't, then this is likely the cause of the problem.

To fix it, you need to fix the permissions. Try Repair Permissions in Disk Utility. If that doesn't work, try the following:

1) Delete that file while Safari is running - then go into Safari and add a new bookmark. This will create a new bookmark file with all your bookmarks.

If you delete the file while safari is not running you lose all your bookmarks - so make a back up of the file. The safest thing is to rename it.