I have deployed our application using clickonce and signed the manifests using a code authorizing certificate and installed the application on a number of computers.

Sometime (not alway) when I deploy a new version of the application the update terminates and says that the manifests have been signed by different authorities. I am using aThawte Certificate to sign the manifests.

Does anyone have any idea on how to fix this?

This should not happen if you are signing with the exact same certificate. Can you guarantee you did not select a different certificate by mistake when you published the update?

It is definitely the same certificate.

Would it make a difference if I selected the certificate from File and then next time from Store? Note sure if I did this but might have...

I'm pretty sure that shouldn't make a difference. The certificate info should still be the same, unless they are different certs with the same file name... that could explain the problem :-)