I hit the exact same problem when performing clean 9.10 Karmic install
preserving my home directory. I had 7.04, 8.04, 8.10 and 9.04 clean
installations before with no problems. Double-clicking folders on the
desktop would open them implying there was an application registered for
folder mime type. The places menu entries however did not work as per
this bug report. Had to right-click on a folder, select "open with
another program..." and then to pick nautilus as default application to
open "this and other files of type "folder" to fix this issue.

I am not sure if the problem occurred right after install or after
tracker installation and removal (and then I have manually removed
~/.config/tracker file as well). It may worth to look at tracker app as
a potential source of a problem, as it was installed on earlier versions
of Ubuntu by default, and is supposed to index files and folders so it
could possibly affect mimetype list somehow.

Having said that, I never had a problem like this until upgrading to
Karmic.

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opening a directory using an application change associations incorrectly
https://bugs.launchpad.net/bugs/260492
You received this bug notification because you are a member of Ubuntu
Desktop Bugs, which is a bug assignee.

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