Hi,
Yes, both MXI-2 and MXI-3 can be used together in a Windows 2000 system. Two quick things to try are that you are using NI-VXI 3.2 and the steps in the MXI-3 troubleshooting guide (link below). Also, what size is your user window? If it is too large there will not be enough resources for both PXI cards.
In order to suggest anything else, we need to know more about your system. Are you using PXI-MXI-3 or VXI-MXI-3? Can you describe what your set-up is? How are your chassis linked? With that information we can help you further.
Thank you,
Katie S.
National Instruments
MXI-3 Troubleshooting Guide
http://digital.ni.com/public.nsf/websearch/484f81e6570ad803862569ed007aaa41?OpenDocument