the system partition is where the boot files for the os are stored, these ar the files like ntldr, boot.ini etc
the boot partiton is where all the os files are stored that actually load the os are.
so if had two partions (c & d) all the boot files would be on the system partition (C) and all the systems files are on the boot partiton (D)
sounds backwards i know, i think that what happened was the guys at microsoft who designed win 2k went out for a piss up, got hammered turned up the next day when doing the technical write up and got it the wrong way round, but Microsoft never backed down.
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