Check your output folder under "Flex Build Path" options in the properties. Make sure the folder is correct.
Everything is set up correctly with the path folder - as this error occurs with an empty, blank, default AIR app built via "new".
I believe this is an error with 4.0.1 - as when I installed 4.5 demo (on OS X); this problem doesn't exist and I had no problems building an AIR app.
So either there's a problem with my version/copy/install of Flash Builder or it has something to do with the AIR/FB/and VMWare/Win7.
Can you post the contents of C:\Users\Adobe Flash Builder 4\test2\bin-debug\test2-app.xml? The error seems to indicate that AIR did not like something about the application descriptor file.
P.S: 4.5 Builder with 4.5 SDK is the recommended setup.