I have run into a similar problem to the on encountered here: How to sign code (.EXE file) with a .SPC or .PEM file from GoDaddy (using Ubuntu)?
I have used both the MONO signcode tool (https://developer.mozilla.org/en-US/docs/Signing_an_executable_with_Authenticode) and osslsigncode (http://sourceforge.net/projects/osslsigncode/files/osslsigncode/) and the executables show a digital certificate present signed with "Go Daddy Class 2 Certification Authority". When I view the certificate details it says "No signature was present in the subject" I have tried with the timestamp server and without the timestamp server and there is no difference. I am running the code on Ubuntu Precise and testing on Windows 7.
Suggestions?