Cluster Alignment for NTFS vs. FATOn NTFS volumes, clusters start at sector zero; therefore, every cluster is aligned on the cluster boundary. For example, if the cluster size was 4K and the sector size was 512 bytes, clusters will always start at a sector number that is a multiple of 4096/512 — for example, 8.
However, FAT file system data clusters are located after the BIOS Parameter Blocks (BPB), reserved sectors, and two FAT structures. FAT formatting cannot guarantee that data clusters are aligned on a cluster boundary.
In Windows 2000, CONVERT handled this problem by forcing an NTFS cluster size of 512 bytes, which resulted in reduced performance and increased disk fragmentation. In Windows XP, CONVERT chooses the best cluster size (4K is the ideal).