Defrag in two different file system

Hi everyone
I have two HD 40 and 80. When I defragment , I use diskeeper. One HD is in NTFS system file and the other in FAT32. I make backups on a regular basis between C drive (XPhome in NTFS) and D drive (XP Pro in Fat32). Is it harder for my diskeeper that way or not because of the different file system. Also would it be faster to defrag only when I go on my Pro HD. Right now I am all doing it from C drive. Is it normal to share program like that or should I have program installed on each OS to run better? Lots of questions I know

I use Diskeeper as well. All my HDs are formatted in FAT32. I run 2 installations of W2K on the same machine. I installed DK in both W2Ks, and alternate fairly regularly between the 2 OSes. I always defrag the other W2K, never the running W2K itself. It runs nicely in the background and I only know it's running because of the icon in the systray.
DK could not care less what file-system your HD is, as long as it only does one HD at the time.
HTH