For Windows Vista (and Windows 7) there's a policy, you should use that to manage these clients. See:
Computer Configuration \ Administrative Templates \ Network \ DNS Client
Allow DNS Suffix Appending to Unqualified Multi-Label Name Queries
The default behaviour is disabled as far as I'm aware.
Otherwise there's a registry key which can control this depending on the version of Windows.
Windows XP, Windows Vista and Windows 2008
HKEY_LOCAL_MACHINE\Software\Policies\Microsoft\Windows NT\DNSClient
Name: AppendToMultiLabelName
Data: 0 (Do not append suffix) or 1 (Append suffix)
Default: 0
The default value may vary with Service Pack level for Windows XP.
Windows 2003
LOCAL_MACHINE\System\CurrentControlSet\Services\DNSCache\Parameters
Name: AppendToMultiLabelName
Data: 0 (Do not append suffix) or 1 (Append suffix)
Default: 0
Finally, don't expect that to have the slightest impact on NsLookup. It uses its own resolver and is not bound by the rules used by the DNS Client (DNSCache).
HTH
Chris