What are you using to test the dns settings? Linux uses the 'host' command 
and 'dig', Windows uses nslookup. In either case run 'nslookup server 
dnsserver-ip' to see what the database has associated with the name.

My guess is that the Windows computers aren't set up to use the correct 
domain to add the ending part automatically. Have you tried pinging using 
the full dns name (i.e. server.domain.org <http://server.domain.org> versus 
server)

I believe there are two ways to add a domain to Windows computers: Go to the 
TCP/IP Network options for the LAN interface and click on the DNS tab. 
Choose Append these DNS suffixes and add the suffix of domain there.

Or go to System control panel and the Computer Name tab. Click on change... 
and more... and add the Primary DNS suffix for the domain... reboot.

-- 
Jeff Rasmussen
GPG public key 0x9686C12F
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