Wow! nice explanition!
I'm not sure about the virus will run on wine without execute (+x )
permission. Pls some one check it.
I don't run Windows so my my best guess is you are using Wubi or
accessing the ext2/3 through some interface in windows. so your your
ubuntu partionon has bare without the filepermission.
to remove the .exe stuff..
$ find / -name "*.exe" -exec rm {} \;
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