I had the pleasure to troubleshoot this interesing issue and feel this information might be helpful for everyone dealing with code signing. You might hit this when trying to use the same keyset for strongname signing as well as for manifest and/or Authenticode signing.
As noted in this article Visual Studio 2005 cannot handle PKCS#12 files that hold several certificates (the CA chain). But even if you have ensured that only the end entity certificate is present in the PFX file, you might get an error dialog from Visual Studio after entering the passphrase for the FPX file:Title: "Error during Import of the Keyset"
Message: "Object already exists"
Cause:During enrollment (really when creating the keyset and the CSR) the KeySpec parameter has been incorrectly set to AT_KEYEXCHANGE (1). This must be AT_SIGNATURE (2) for Visual Studio 2005 to work.