Windows versions of the Firefox browser have an independent certificate trust store and do not integrate with the native system cert trust infrastructure. This limitation applies to all Firefox versions up to and including 48.
Good news in 2016, software developers at Mozilla are putting the finishing touches on Firefox 49 which should have the issue resolved to integrate with the native Windows Certificate trust store. This will help Firefox compete with Internet Explorer, Edge, and Chrome browsers which already have support for the native Windows cert trust stores. See the following Mozilla bug tracker entry for details:
Organizations using Windows / Active Directory / Group Policy will automatically benefit from this new functionality after migrating to Firefox 49 (once a stable release is available to the public). Firefox will finally be able to trust the same set of certificates as other native Windows programs. I’m hoping this update will also allow the use of user identity certificates from the Windows certificate store? Version 49 is currently scheduled for public availability on 2016-09-13.