We have signed our product installation using SignTool.exe and GoDaddy certificate, and our signature appears valid in windows and using \"verify\" option of SignTool. Howev
I've discovered through trial and error that this is caused by a Windows update that breaks IE:
Cumulative Security Update for Internet Explorer (2870699) - published Sept. 10, 2013
http://support.microsoft.com/kb/2870699
http://technet.microsoft.com/en-us/security/bulletin/ms13-069
I installed all of the latest updates and was able to reproduce the problem. I then uninstalled this single update and it fixed the problem. I then reinstalled the update and it was broken again.
This is bad!