I use UltraMon with dual monitors, and have it set just as you're wanting........
Maybe this is your problem
Dualhead cards and true multi-monitor support on Windows 2000
Due to a limitation in Windows 2000, dualhead cards that use a single chipset to drive both monitors require special workarounds in the driver to be properly recognized by the system. If these workarounds are not implemented, Windows 2000 sees a single large monitor instead of two.
http://www.realtimesoft.com/multimon/faq.asp#TrueMultimon