Been looking into this a little and I thought I'd share my findings.

Most people know that you can convert fat32 volumes to ntfs using microsoft's "convert" program. However, unless that fat32 volume was created using their new "oformat" utility, the first several clusters are only 2k and throw alignment off for the rest of the drive.

This means that convert.exe will make your clusters 512bytes, which slows performance.

To remedy this you can use a utility (bootit ng) that shifts all of your clusters to the proper alignment.

There is a page here that explains this process in more detail.

The program is shareware, but the 30 day trial gives you plenty of time to make the boot disk that I assume doesn't expire.

I use partiotion 8.0 from powerquest!

I use convert if i have to...works good for me.