That bug has been described on https://launchpad.net/distros/baltix/+bug/41256

"I use fresh dapper (2006-04-25) and in my opinion adding to favourites doesn't work properly in nautilus - it is not intuitive and doesn't work as user would expect.

Little example:

Open Nautilus

create ~/test directory
go this directory and create two subdirectories:

~/test/1
~/test/2

Stay in this directory - click on ~/test/2

This directory will be highlighted

Then hit Ctrl-D

The directory that will be added to favoutites is ~/test not ~/test/2 that we highlighted and we expected to bookmark.

In my opinion that's wrong behaviour.

Ctrl-D shouldn't work on parent element it should work on currently active and highlighted element.

And more - I think that "bookmark" shortcut should be available in context menu on right click.

In this way user could select directories that want's to bookmark from his list of visible dirs.

For example - I got ~/test dir
and ~/test/1 ~/test/2 .... ~/test/100 dirs
then I go to ~/test and select directories that I want to bookmark by highlight them and right click + bookmark action on selected dir.

Currently to bookmark I should go _into_ directory that I want to bookmark and Ctrl+D.

This is non intuitive, time wasting and wrong behaviour.

Also bookmarking should work on multiple directories. So I should be able to select directories with mouse click with Ctrl or Shift to select range and then bookmark more than 
..."