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Reply received from Certificate Issuer:

Greetings from Comodo.

It would appear you've signed the file correctly, however the problem deals with expansion of existing Microsoft functionality built previously into IE 9 and brought to the Desktop for Windows 8.

Windows 8 SmartScreen defaults to requiring admin approval for unrecognized applications. Since your app is signed by a new certificate that Microsoft has never seen before, it must re-establish its reputation within the Microsoft ecosystem.

SmartScreen application reputation uses a algorithm to rank the probability that a download is legitimate software and uses a file's hash which identifies the file contents and its digital certificate to determine whether it's a known application with an established reputation.

If the application reputation algorithm ranks the file as unknown perhaps because the hash value hasn't been seen before IE9 and above with throw up a warning when users try to run or save the file.

A Microsoft database is checked (via an Internet connection) and updated with each install of your program. The reputation score for your signing certificate increases over time and eventually the SmartScreen warning goes away.

Microsoft also suggest and recommends that publishers sign all applications with the same digital certificate to help better expedite reputation gains.