Certificate prompt appears in wrong user session

We are experiencing a weird issue with two different website that require a private certificate that is installed in the personal certificate authority and another key another in the intermediate certification authority.

the problem is two different users have a personal certificate each, which is installed in their certificate store on  a Windows 2012 R2 remote desktop services server using session host.

One user can successfully use the certicate with no issue, however the prompt to allow the website to open on the other users profile appears on the administrator user session and not their own, how do we resolve this?
safemode_nzAsked:
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CoralonCommented:
Did you install the intermediate certificate in the User account or the Machine account?
It needs to be in the Machine account, so that everyone on that system can have their personal certificates trusted.

Coralon
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safemode_nzAuthor Commented:
thank you very much for your help
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