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My first guess is that someone found a big hole in Active X controls that lets a malicious programmer deep into the client's system. MS has had some minor problems in that area several times since the launch of 5.5. It's just a guess, however.
Integrate the browser too deeply with the O/S and you just might open up a can of worms.
gmiller, when did you first learn about MS pulling Explorer? Is it related in some way to the recent hacker attacks?
It's like the elephant standing in the middle of the room that no one will mention.
Microsoft temporarily halts IE 5.5 downloads [infoworld.com]
Downloads of MS IE 5.5 halted temporarily [zdnet.com]
-- you've got to wake up pretty early in the morning... ;)