I was able to learn more about this issue. The intermediate certificate 
was not chaining to the root certificate using 
security.enterprise_roots.enabled or in the manual certificate import.

Despite the intermediate being in 
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\SystemCertificates\CA\Certificates 
and the root ca being in 
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\SystemCertificates\ROOT\Certificates 
, it was not until I manually exported the CA\Certificates, changed its 
reg path to ROOT\Certificates and reimported that the feature worked. 
Similarly, the manual certificate import in firefox did not need the CA 
imported, only the intermediate.

Does this mean that our intermediate isnt signed properly (according to 
nss) by the CA or firefox is having issues connecting chains?

Windows happily puts the intermediate into the intermediate store and the 
ca into the root store and the other browsers respect the chain. 
Unfortunately, the site and keys are private so I cant share them.
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