The DOS window's property called "QuickEdit" should be unchecked so that the mouse will work in the DOS window under Windows 2000. Have you gone back into the properties of the DOS icon and verified that it was saved and stayed unchecked? Also, if you have multiple DOS icons such as on the desktop, program tray or Start menu, then be sure each of them are updated.
You can read my complete post at thread290-590977 about this and other issues.