Well I am no expert on this specific topic, but to me it sounds like you may have potential problems with OS clashes. If you're running both NT4 and 2k on the same partition, some shared files may be optimized for one OS but not the other. Windows 2000 was built on windows NT and therefore shares some structural and file name similarities. However, siince windows 2000 is a newer OS it may have replaced some files wich maybe win2k optimized, but which NT4 struggles to handle!
I REPEAT: I AM NO EXPERT ON THIS SUBJECT, but I do know one thing, it would be a better idea if you allocate each OS its own partition. I don't know whether or not that's practical or even feasible in your case since you've already installed both OSs on one partition. In the future though, if you wish to dual boot ANY OSs, you really should set up seperate partitions for them to work in. That way you can prevent clashes and improve performance, and also organize them better!
good luck. I hope this helps!