Try to manually delete the directories which create a problem:

sudo rm -rf /usr/lib/dynare/mex/2007a /usr/lib/dynare/mex/2007b

And then retry to configure the package.

This is a bug which has been fixed in the Debian version of the package,
but the bug fix has not been merged into Ubuntu.

Regards,

-- 
package dynare-matlab 4.0.3-2 failed to install/upgrade: 
https://bugs.launchpad.net/bugs/465436
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