I had the very same problem.

Actualy digging and digging and digging in a lot of forums, I found that
the error has to do with pcmanfm. The file manager is broken, and even
if your mime-types are updated, it will not recognise *any* file
(pcmanfm does also manage the desktop).

The solution I found was to download version 0.5.2 from:

http://sourceforge.net/projects/pcmanfm/

And compile it.  It is necessary to install various development packages
(hal, hal-storage, gain...) through Synaptic.

$ ./configure
$ make

It will complain about a missing '\n' in the translation file ca.po. cd
into po and enter the command:

$ pico +298 ca.po

In the previous line, add a '\n' before the last '"'.

$ cd ..
$ make
$ make install
$ cd /usr/bin
$ sudo ln -fs /usr/local/bin/pcmanfm
$ killall pcmanfm

Press [Windows]+R and type: "pcmanfm -d"

Everything should work now.

The obvious fix to this error is to upgrade package in Ubuntu.

-- 
file icon handler doesn't remember the file association
https://bugs.launchpad.net/bugs/456266
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