I am working on deploying a ClickOnce Application build on .NET 4.5 Here are the facts:
Check whether your application manifest is being used for trust information (i.e. publisher name). If it is, make sure the publisher name matches who the certificate was issued to EXACTLY. If it does not match, you'll get an "unknown publisher" issue. This setting is located in Visual Studio in the "Publish" Tab. Click the "Options..." button, followed by the "Manifests" list item.
Try unchecking the "Use application manifest for trust information" and republish to see if the issue is resolved. If you do need the option checked, click the "Description" tab and make sure the "Publisher name" value matches the value of the name the code signing certificate is issued to EXACTLY.