2 B honest, I've never trusted the converter included with Winblows. Too many complaints about performance issues after running it. You also can't revert back to FAT32 if you don't like how things turn out. You might want to invest in a copy of Partition Commander or Partition Magic.
I personally use Partition Commander from a "DOS" bootable CD (actually, I think it's Linux....but you get the idea). It takes extra precautions to protect your data during the transfer and has a roll back feature to take you back to FAT32 if anything goes wrong. You can also adjust your cluster sizes and other nice goodies to optimize your disc usage. It can even manage Linux partitions as well. It's a worthwhile $25-$30 investment for the peace of mind. It also doubles as an excellent drive copy utility when you go to a larger/faster hard drive.
If it ain't broke don't try to fix it! But, hell if you can tweak that bastard just a little bit more....hehehe.