To benifit other users, posting what we did on this:
We worked on this offline and looked at the configuration of SSL. (Server Windows 2000 SP4 - IIS 5.0).
The actual error we’re seeing in the SSL Diagnostics tool is, "You have a private key that corresponds to this certificate but CryptAcquireCertificatePrivateKey failed."
This almost always means there’s a permissions problem accessing the private key, which is stored in the MachineKeys directory. We checked and verified the permissions and ensured that all machine keys prems are good (KB278381), but it still didn't work.
We checked the certificate which was sent by Verisign - It was in p7b format?? - It shows it has private key - but does not allow the export private key. From IIS certificate Wizard, everytime we tried to complete pending request with certificate that was sent by verisign - We see "Keyset does not exist" error.
Test certificate from SSLDiag - Works fine no issues with that at all. Issue seems to be with Verisign certificate but does not have enough evidance.
Finally after some troubleshooting instead of finding out the root cause - We concluded to take a back up of IIS metabase and re-install IIS as there are only few sites running on this box. Stam to take a call on re-installing IIS.
~ Ganesh