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I've had this happen twice now: I boot to win7 in boot camp, and install the windows updates as indicated by windows. After rebooting , osx loads slowly at first, and disk util tells me there are errors on mac partion. I rebooted to RestoreDisc where disc utility says it cannot fix errors and to format whole disk! I booted into Windows again, and saw that there is a temp folder on the mac partition full of windows executables! Now I have read that win7 updates will write to any adjacent partition, using it as a swap drive!

UPDATE: I just decided to not continue punishing myself and got Parallels7. Apparently W!ndow$ uses the next partition as a swap drive regardless whether it has access or not. ugh.

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I haven't tested this, but my understanding is that you can avoid this problem by dismounting the OS X volume before running Windows Update. This Mac OS X Hint suggests using the mountvol command to mount & unmount the volume. This Apple KB article suggests temporarily disabling the AppleMNT.sys driver and rebooting.

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Thanks, but I went with the VM solution. It just feels less painful. –  callisto Apr 20 '12 at 10:07

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