I would personally always stick with NTFS unless you have an earlier version of windows installed on the PC and need to access the drive
If you have FAT32 partition you can convert it to NTFS using either the command line or windows but it cannot be converted back to FAT once converted to NTFS
in response to 5th's comment I would probably recomend that you pull a HDD out of the PC and just stick it in to another Windows XP/2000 PC but if you don't have one available then you can use BART PE as a last resort, I always keep a copy handy for use on problem pc's as it is probably the easiest way to boot and read a dodgy NTFS without another pc handy
(Bart PE basically takes your windows disk and creates a CD that you can boot into a cut down version of windows XP from although as it uses a virtual disk it can be pretty slow on a machine with not much RAM )
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