IE9 SmartScreen Warning, Despite Following All Recommendations

Question

We offer a Windows program downloadable as an InstallShield EXE from our website.

When someone running IE9 attempts to download and run our software, they see the follow

Answer 1

Extended Validation Code Signing Certificates don't suffer from the need to build reputation slowly according to this post:

Reputation is generated and assigned to digital certificates as well as specific files. Digital certificates allow data to be aggregated and assigned to a single certificate rather than many individual programs. Although not required, programs signed by an EV code signing certificate can immediately establish reputation with SmartScreen reputation services even if no prior reputation exists for that file or publisher. EV code signing certificates also have a unique identifier which makes it easier to maintain reputation across certificate renewals. Only Authenticode Certificates issued by a CA that is a member of the Windows Root Certificate Program can establish reputation.

At this time, Symantec and DigiCert are offering EV code signing certificates.

In an effort to improve my answer, I've added a link to a similar question I asked and eventually answered myself.