At one time there was a direct statement on the Lyon Court home page (under their "clans & tartans" subheading) that while the Lyon Court would record a chief's tartan if requested, that the Lord Lyon had no direct authority over tartan and it referred tartan enquiries to the Scottish Tartans Authority.

However, I just looked and I no longer see that statement. I think the entire "tartan" section of their web site is under review now that the National Register has been established.

If it will help, there is an excerpt from the book District Tartans by Teall & Smith, on the Scottish Tartans Authority web site, that deals with the Lord Lyon and tartans.
http://www.tartansauthority.com/web/...y/LordLyon.asp

I've also dealt with the subject in one of my Scottish Banner articles, archived here:
http://albanach.org/tartans_heraldry.htm