MSCONFIG is not supplied with 2000 Pro. I use STARTER (search these forums).
What I don't read in your post is a note about if you finished the 2000 install with the drivers for the machine. Microsoft doesn't supply them.
I am trying to add windows 2000 pro to a win98se computer and am having a number of issues getting the os to work. Right now trying to either restart or shutdown from 2000 I get the window showing shut down. It clears leaving a blank blue screen with only a mouse pointer showing. There it hangs. Computer reboots etc ok in safe mode and in win98. I tried the msconfig trick that I use with win98 to selectively uncheck some start up programs except 2000 does not recognize the command. What I would appreciate,in addition to suggestions on the shut down problem, is a listing of some of the commands useable from the run window. So far regedit and sysedit work. Sfc does nothing and I can not delete it. Msconfig, windows cannot find nor can it find winipcfg. Haven't tried any thing else.