Shaunjurr has the right idea....mixed is not really the way to go unless you have some application that absolutely requires is.
Your filers should be joined to your domain, if you have multiple, I hope they all trust one another.
Your filers need to be bound to LDAP.
if your usernames are the same in LDAP as they are in AD, simply run wcc -s DOMAIN\USERNAME to see if you are resolving properly. If you put in mydomain\myuser and you see something to this effect, you are probably good to go:
(NT - UNIX) account name(s): (mydomain\myuser - myuser)
***************
UNIX uid = 1055
user is a member of group users (100)
user is a member of group users (100)
NT membership
BUILTIN\Administrators
BUILTIN\Users
User is also a member of Everyone, Network Users,
Authenticated Users
***************
Verify all the NT/AD memberships for the user are correct and there you go. Otherwise you need to read up on the usermap.cfg file.
One thing to be sure you avoid if you have NTFS style permissions is setting ownership to creator/owner on files/directories. This seems to throw *nix systems off, I believe due to the fact that creator/owner is actually a wrapper and thus *nix has no way to map it back to anything viable.