We manage the subdomain website
subdomain.example.com A completely separate company manage
www.example.com which has a separate analytics account that we do not have access to.
We've noticed that traffic from the main website seems to be showing up in Analytics as direct traffic (destination URLs match up and it is WAY higher than direct should be for this site), and isn't showing as a referral.
I can't work out why this would be the case.
Speculation: I've noticed that the main website has three analytics codes on it, all for the same account. I've advised this is changed urgently to keep only the universal analytics code. Could this be something to do with the issue?