Version 3.1 of the NTFS file system changed the location of the Master File Table and two metadata files and modified the header information in the file records. This was done to improve performance.
When you upgrade a Windows 2000 or NT machine, any existing NTFS volumes are upgraded to NTFS 3.1. You are not asked for permission and there is no workaround. If you dual-boot between operating systems, make sure you are running NT4 SP6a or Windows 2000 SP1 or later. If you fail to take this precaution, you risk getting blue screen stops when attempting to boot in to the earlier operating system.
The following additional new file system features have been added or modified in Windows Server 2003:
Improved defragmentation. ...