Security Essentials detecting threat in wyUpdate

Since the latest Windows update Tuesday, some of my clients are reporting that my app is being "deleted" with the shortcut. After careful analysis it seems that Microsoft Security Essentials is tagging my app with a trojan because of wyUpdate. The problem seems with wyUpdate updating a SystemCertificate registry, here is the problem:

http://d.pr/i/144Ir

Thanks in advance

wyUpdate doesn't touch that registry. It's open source, you can see for yourself: https://github.com/wyattoday/wyupdate

Never use "custom versions of wyUpdate". Always use our pre-built version of wyUpdate. If it's not code-signed with our signing certificates, then it's not supported (and probably dangerous).

What if I don't use a custom version?

It's weird, we never changed the wyUpdate.exe, and I think this is the latest version:

http://d.pr/i/17Hgx

Right click wyUpdate.exe, click properties. Is it code signed? If not, then they're not using a valid version of wyUpdate.

If it is code signed then, and you're not modifying that registry entry as part of your app, then it's a false positive by the AV.

Thanks Wyatt, it is code signed. So I guess it is a false positive. I'll keep investigating and I'll let you know.