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The issue isn't making that huge of a partition FAT32, it is quit easily done. In fact you should be able to make a FAT32 partition of 2TB. The issue is the efficiency you are sacrificing due to creating such a large partition; the cluster size in FAT32 is 32KB for anything above 32GB. NTFS is far more efficient in this aspect, with only a 4KB cluster size. Though honestly you shouldn't have much of an issue because most of your files on the HD are going to be rather large (I'm assuming... movies and tv episodes :D) so you are not going to see much of a problem. You will see space ‘wasted’ in a FAT32 setup that large but you’ll only run into issues if you use it store pictures on it or other files that are fairly small.
I want to get a system like that lol. I've been having nothing but trouble recently out of my media center computer. It hates my 52" RP HDTV, I can't get the resolution set correct using either hi-def connections yet it looks "perfect" using the S-video connection. May just wanna get something like you have, sounds like it will be much less of a head ache in the end.
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