Answered: java.lang.Exception: Public keys in reply and keystore don't match

Did you create the CSR with keytool?  If not this could be one reason for the error message above.  
If you could outline the steps you took to generate the CSR then outline the steps used to import the issued certificate I can help you trace down the issue.  Just sending the error message and no details of how you generated the error make this process extremely difficult since there are many reasons why you could receive this error message.