Hi, generally converting drives may make them slower because of MFT fragmentation, however that can be easily remedied by using a trialversion of diskeeper or O&O defrag and running a offline defrag. There is the issue of certain programs, the more elderly ones, running slower under NTFS, but this is rare these days. Other than that the only other reason that a drive maybe slower after NTFS is that there is either a fault with the drive, the data on it or a old drive. It is accepted that NTFS is faster than FAT32 on drives larger than 400mbs, and especially on drives where the files and volume size increases.
Taken from XP myths: http://mywebpages.comcast.net/SupportCD/XPMyths.html
Myth - "The FAT32 file system is better than NTFS."
Reality - "NTFS is the better file system with many advantages over FAT32. NTFS features: Built-In Security, Recoverability, Alternate Streams, Custom File Attributes, Compression, Object Permissions, Economical Disk Space Usage using a more Efficient Cluster Size and Fault Tolerance. Windows 2000 and XP come with NTFS version 5 which includes even more advanced features such as: Encryption, Disk Quotas, Sparse Files, Reparse Points, Volume Mount Points. None of which is available with FAT32." - Comparison Chart
NTFS is built for speed with impressive disk I/O performance on large volumes (Over 400 MB). NTFS uses a binary tree structure for all disk directories, which reduces the number of times the system has to access the disk to locate files. This system is best for large directories, and NTFS easily outperforms FAT32 in these situations. In addition, NTFS automatically sorts files in a folder on the fly. NTFS gains an edge over FAT32 by using relatively small disk allocation units (cluster sizes) for NTFS volumes. Smaller clusters prevent wasted disk space on volumes, especially those with numerous small files. Because NTFS uses small clusters better and has a more efficient design, its performance doesn't degrade with large volumes, in contrast to FAT's. As the number of files and volume size increases NTFS performance is not effected but FAT32 continually gets worse. - Gaming Performance
In addition to its extensive memory and application protection features, NTFS is a reliable file system. When storing data to disk, NTFS records file I/O events to a special transaction log. If the system crashes or encounters an interruption, NTFS can use this log to restore the volume and prevent corruption from an abnormal program termination or system shutdown. NTFS doesn't commit an action to disk until it verifies the successful completion of the action. This precaution helps prevent corruption of an NTFS volume. NTFS also supports hot-fixing disk sectors, where the OS automatically blocks out bad disk sectors and relocates data from these sectors. This housecleaning happens in the background. An application attempting to read or write data on a hot-fixed area will never know the disk had a problem. I only recommend and use NTFS with Windows 2000 and XP." - Source