Drive letters reassigned

Long time after upgrading from NT 4.0 to Windows 2000 Server, my drive letter assignments have been changed around. Previous to the upgrade, NT 4.0 was installed on the C: drive,Now its D:.
even the CD-rom drive has also changed.
Now there is no C: letter assigned. I cant change the letter assignment from Disk manager because it says that it is a system partition.
Has anyone else experienced this reassigning of drives? Any Idea.
Thanks,