Just to note that I just uploaded a new minimal Windows installer -
Avogadro-0.9.5-win32a.exe, this contains a two line patch to OpenBabel
which Tim figured out after much hunting around. There will also shortly
be a new Python enabled installed - Avogadro-0.9.5-python-win32c.exe.
https://sourceforge.net/project/platformdownload.php?group_id=165310&sel_platform=16779
So many thanks to Tim. I would encourage all Windows users to update to
one of these two versions. I think after much hunting we have tracked
down the file reading and writing issues. Please let us know if you spot
any more issues. We would really like to track down any issues like this
on any platform we support as we move from beta to stable release.
As we move through our last month in beta we would really appreciate as
much testing as possible. This is perhaps most needed for the Windows
port as none of our development team use are full time Windows users.
Tim and I have put a lot of time into improving the Windows port, but
neither of us is willing to bite the bullet and give up Linux…
So please test, provide detailed bug reports. We wouldn’t mind the odd
compliment either 
Best wishes,
Marcus