Certificate Alert in browser though Cert is "Always Trust"

[monogrant]

Using a Configuration Profile I've deployed a certificate (tried both Computer and User level) and have verified in Keychain Access that the trust is "Always Trust" across the board - looks like the config profile is working. When I access the site this cert is issued from (internal Extensis Portfolio Server) Safari still pops up the alert to accept and Chrome flags the site as unsafe.

I've attempted reboots, logout/in, etc. but I can't seem to get this certificate alert to be ignored by trusting this certificate.

Is there a way I can force prevent this alert for a self-signed cert?

[calumhunter]

is the cert an intermediary? Perhaps you need the cert for the root ca that signed this cert also to be in the keychain and trusted

[davidacland]

Sounds like there are missing bits of the cert chain to me.

Alternatively there is something else wrong with one of the certs in the chain. Perhaps one has expired?