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Yahoo! Search Technology actually powers MSN. This is a hybrid "best of breed" technology from Inktomi, AltaVista and Fast.
MSN does not take any paid inclusion lisitings - including those which were submitted through Inktomi Site Submit or Overture Site Match. Hence the set of results that are feed to MSN is smaller than the result set used at Yahoo!
Many people are seeing that it takes a bit longer for your URLs to show up in the MSN results after being spidered. This could be that the index is not refreshed as often for MSN as it is for Yahoo! However, I am yet to see any positive proof on this.