I used to have the same problem with Win2k. It happened when you format Linux partition using FAT32 or anything that Windows can recognize, the same thing happen when you put partition type as Windows recognizable format even when you're not formatting them. When you run Win2k, it remembers hd layout and assign drive letters to each of the recognizeable partitions, although you haven't format them, what a SILLY Windows! And this drive letter will remain until you changed it or another hd inserted...
When you format Linux partition, that is changing from FAT32 into ext3, Windows still claim that partition as FAT32 and trying really hard to read them, (I don't understand what the sake M$ do? Why don't they check the signature?) and QUELLA! you have a turtle Windows!!
To avoid this problem, before installing Linux, make sure you remove all drive letter assignments with drive manager from Windows, this will make Windows doesn't check them at boot time nor claiming them as FAT32 and trying hard to read them...
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