Why the hell do you have 64k cluster sizes? Now days a hd with 64k cluster sizes should only be seen on 500+ gb hard drives (if there is such a thing). Using 64k clusters is very inefficient use of your hard drive especially if you are going for optimal performance.
From your post, it sounds like you are now sure what it means to defrag your comp, here we go: When you write to your hd, it writes files one after another from the inside out (i think..., it's not important) as the platter spins, putting the data into induvidual clusters, if the file is 100k, it uses 2 clusters(when using these 64k clusters). Now if a month later you go and delete this 100k file after saving more data, there is this gap between all your saved data. The next time you save a file (say it's 150k), it is written there until those 2 clusters (128k) is taken up, then it jumps to the next available cluster on the hard drive. With multiple files splitted up into many pieces, it can be cluttered, and at this point, your hard drive is fragmented. When you defrag, your computer is taking these spaced out chunks of your file and re-writes them so that they are all in clusters that are lined up one after another. When your hard drive is defragged, it doesn't have to skip all over the place finding all the individual chunks of your file, thus more efficient. (I hope that isn't confusing, if it is, tell me I'll explain more)
The reason your computer is having problems or simply will not defrag your hard drive is because it would be very processor intensive for your computer to be moving multiple 64kb clusters around your hard drive instead of just 2kb clusters. I think you're kind of confussed on the concept of clusters, trust me, the smaller, the better (for once, some people got to hear what they wanted).
Also, when using 64k clusters, and you save a 129k file, it HAS to use 3 clusters. And that's 63k of hard disk space wasted, it cannot be used until that file is deleted, and that cluster is freed. For this reason it would be more wise to use 2k (FAT 32) or 4k (FAT 16) clusters. I am also using a 40 gig hd split into 3 partitions that are all each FAT 32. Using smaller clusters will more efficiently use the disk space you have.
QUOTE:
"but are there any drawbacks to running a DAW w/ NTFS on the OS drive and FAT32 on the audio drive?..."
There shouldn't be any drawback to storing your OS on the NTFS drive and FAT 32 on your music drive. But using the FAT 32 (2k clusters) in place of the 64k clusters will be a godsend.
QUOTE:
"i'd still like to know if there's a file system i can format it to that will allow me to defrag? (does anyone have a FAT32 drive w/ 64k clusters on a Win2K system?)"
The FAT# (File Allocation Table) doesn't describe your drive exactly, it describes the size of the clusters. FAT32 has 2k clusters.
QUOTE:
"several of my files show up as having 2 or more fragments. is this not a problem on a 7200 RPM?"
The speed of your hard drive should play no part as to whether a file is fragmented.
QUOTE:
"i'd assume unfragmented files are the best way to ensure sample-accurate playback "
Correct. It would help prevent uninterrupted playback.
I would recommend that the next time you back up your music drive, you reformat it, using FAT16 (4k clusters) for one partition or FAT32 (2k clusters) for more than one. Also, defrag once a week using, Windows' generic defragger, if this is a drive you edit a lot. And with this you should get optimal performance (even though you experience no problems yet). I hope this lengthly post answered all of your questions and doubts, if it didn't I would be glad to explain more clearly.