There's an issue with the new release of MOPAC2009 : Avogadro freezes when I want to render MOs.
I found out the AUX file does not contain all the eigenvalues and occupancies that Avogadro needs.
I would suggest to adapt Avogadro to this new AUX file shape and/or always add "LARGE" as a MOPAC keyword to generate the old-shape AUX file and avoid the problem.
Please find attached a zip file that contains the AUX files generated from the same MOP file using two different versions of MOPAC2009.
AUX and MOP files
I will look into this, I didn't realize he had modified the output file and do not have access to the latest version.
This should be fixed for 1.0.2, at least with the LARGE keyword.
http://review.source.kitware.com/1342 contains the simple fix, like I said in the commit message, I am working on a fuller fix but this at least restores the previous behavior. I tested it locally, and it looks good here.
I merged in the simple fix, and will finish off the fuller patch later. This will resolve the immediate issue for you, and will make it into our next release (1.0.2).