hi, i think you thought it out quite good, and i agree with the guy who said that Windows probably prefere to have the HD placed as nmbr one in the chain.

If that doesn't solve your problem i can only guess on MS_made incompabilty_Problems. F.ex like using dualboot on your first partitions MBR.

It will crash, soner or later, at least that is my experience and as far as i've been able to guess it seems to have to do with XP trying (??)to correct what it sees as a corruption of the MBR after you installed your linux. A ting that MS dont seem to give to high a priority to fix.. . And W2000 is a predeccisor to XP, both use the NTkernel even if somewhat changed depending on OS.

btw NTFS on slave and native linux on your master ?
In that case one would expect W2000 to ignore your Master as it wont be able to see/use it. Or it somehow checks out that is on a slave wich probably will give strange results.