I have just installed nautilus-gksu, version 2.0.0-5ubuntu3 (described as 
"latest" in Synaptic), on Intrepid.
I too had to run "killall nautilus" to get the link in the context menu and I 
also get a second window displaying my home directory when attempting to open a 
folder.

The only "funky" thing I've done to Nautilus prior to this is add a
couple of scripts (from the Ubuntu Community Documentation page on the
subject) into my nautilus-scripts folder.

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nautilus-gksu stopped working in hardy
https://bugs.launchpad.net/bugs/201462
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