Hello,
we are not aware of this behavior/issue.
Each enrollment of a certificate (a new login) should always overwrite the key and certificate in the Microsoft store. I have successfully tested this with SSO 2.0 SP 6, IE 11 and Java Plugin 1.8.
If you can not solve this issues, please create a support ticket so we can analyse the root cause of this. Please add java plugin traces and the used Browser and OS version and java plugin version to the ticket.
best regards
Alexander Gimbel