This is caused by the ShadowLoopBack function of Windows 2003. To stop this behavior from occuring a registry modification is needed.
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\MRxSmb\Parameters] "CscEnabled"=dword:00000001 "DisableShadowLoopBack"=dword:00000001
With this setting defined, files copied to the Windows 2003 machine can be stamped with the correct source file time and date stamp and this problem will stop occurring.
This was supposed to be fixed in Windows 2003 Service Pack 2 but some machines still display this incorrect behavior and need this registry fix.