Same here.
I've installed Intrepid this moring, fresh install in /  mounting my /home 
partition during the installation process.

My parasitic application was F-Spot:

[Added Associations]
x-content/blank-cd=nautilus-cd-burner.desktop;
x-content/blank-dvd=nautilus-cd-burner.desktop;
application/x-bittorrent=deluge-torrent.desktop;
image/png=eog.desktop;ooo-draw.desktop;inkscape.desktop;
application/x-executable=wine.desktop;nautilus-autorun-software.desktop;
application/octet-stream=gedit.desktop;
application/x-extension-bin=nautilus-autorun-software.desktop;
inode/directory=f-spot-import.desktop;nautilus-folder-handler.desktop;userapp-nautilus-MKNLJU.de
text/x-python=gedit.desktop;

As you can see, the "Open with" workaround didn't work for me because
the result was appended and not swapped.

Fixed changing the line to
inode/directory=nautilus-folder-handler.desktop;

Thanks.

-- 
opening a directory using an application change associations incorrectly
https://bugs.launchpad.net/bugs/260492
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