Problem signing code for application with embedded runtime

Hi,

I have an Adobe Air application which I am publishing with the runtime embedded.  There are lots of reasons for publishing this way.

I have already seen an unknown publisher message after signing on Windows 8 and a tester reported the same thing on Windows 7.  According to the cert issuer (DigiCert) I need to have an Extended Validation (EV) certificate to get by the Windows 8 issue, but there was no explanation on the Windows 7 issue. 

As the windows file is essentially a folder wiith ".app" appended to it's name, I'm not sure how signing (which I am doing with the Signature tab on the Flash GUI) ensures that the executable contained in that file is signed.

Can anyone tell me anything about code signing when publishing an AIR application with embedded runtime?

Best,

Chris McLaughlin