Each update had a different 'steam.inf' file with the second update being a fix for the first. I don't see what your big problem is, the update process works fine except for the the few hiccups with the content servers.
Heh, for you may be - three hours later my hldsupdatetool is still just stuck on "Checking/Installing 'Base Source Shared Materials' version 4"!
-- trog
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