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On a freshly formatted install of an NTFS partition, the MFT (Master File Table) is created at the beginning of the disk and about 12.5% of the disk space is reserved for it. When you convert, it ends up wherever there is free space, and ends up fragmented. Having cluster sized below 1024 bytes (1k) will also allow the MFT to fragment. Larger than 4096 (4k) clusters will cause disk compression and some third party disk maintenance programs to no longer work.
So what's the big deal about the MFT anyway?
The MFT stores all the information about file location and their attributes for the partition it is on, like an index of the volume. Any file on your drive must access the MFT. As your MFT gets more fragmented, your disk performance will degrade. It can get VERY slow if the MFT is very bad. Even if the files on your drive are contiguous, if your MFT is fragmented, your disk will take extra I/Os to access the file.
Many utilities that defragment NTFS volumes cannot move MFT entries. Diskeeper can defragment your MFT, though. MS Defrag cannot.
Due to the difficulty the MFT can cause, I always recommend starting from scratch with your NTFS partitions.
FAT 32 partitions are more efficient for small disks, due to the extra disk resources the NTFS requires.
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