I'm having the exact same problem with Samba3. (Just posted it in fact).
I don't think Samba supports virtual domains, only virtual servers under 
1 domain.  What a BUMMER!  How is that "virtual"??? :-)
Alex
Grand Titus wrote:
> Hi
> 
> My config: Samba 2.2.3 & Linux Debian Testing kernel 2.4.20
> 
> There are two network cards on my pc :
>     -one links to the network R1 (138.231.121.12)
>     -one links to the network R2 (192.168.0.1)
> I would like to open two shares:
>     -the first one on R1 in the workgroup wkgrp1
>     -the second one on R2 in the workgroup wkgrp2
> I read that, thanks to the directives "netbios aliases" and
"include", it is
> possible to run 2 servers on 1 machine.
> 
> Here is what I have done:
> Extract from smb.conf:
> [global]
> #Configuration for the 'reel' server on R2 (a local network)
> workgroup = wkgrp2
> interfaces = 192.168.0.1/255.255.255.0
> bind interfaces only = yes
> hosts allow = localhost 192.168.0.
> local master = yes
> os level = 33
> domain master = yes
> preferred master = yes
> # Run the virtual server
> netbios aliases = titus
> include = /etc/samba/smb.conf.%L
> ...
> 
> Extract from smb.conf.titus:
> workgroup = wkgrp1
> interfaces = 138.231.121.12/255.255.255.0
> bind interfaces only = yes
> hosts allow = localhost 138.231.121.
> #On this network there is already a master
> local master = no
> os level = 16
> domain master = no
> preferred master = no
> [images]
> path = /home/rezo/images
> comment = Qq images
> browseable = yes
> writable = no
> guest ok = yes
> 
> 
> Unfortunately it doesn't work. The two servers appear in the same
workgroup:
> wkgrp1. It seems that all the global directives in the smb.conf.titus are
> ignored.
> What is the pbm?
> 
> Thanks
> 
> 
> 
> 
>