I have that same type of problem on my old "main" comp..which was WinME...it started right after I installed somethign but I cant remember what....maybe after I partitioned into 3 partitions with Partition Magic.
But it doesnt do it everytime, just once in a while...it will open up a window as if I had clicked on one of the partitions in "my computer". Sometimes its one partition, sometimes a window for all 3, lol.
One thing you could try, if nothing else just for future convenience...is a cool little program to substitute for "msconfig" which isnt on Win2k is
Startup control panel ...its really cool and it shows more thigns than msconfig does anyway...POSSIBLY it could help you find the issue.
Also I wonder if you could try a "bootlogged" startup. (I think thats what its called). ...where it makes the bootlog.txt file showing all the stuff starting etc....maybe some clues there.
JP