It is very simple , actually,
What Behe does is say 'We can not understand how this happened, so therefore it was done by an intelligent designer (wink wink, god).
However, in his original book, every problem he came up with that he proclaimed to be 'Irreducable complex' has been shown to have a well defined path. They were problems that were currently were being worked on when he was writing his book. They have been solved.. indeed, at least one of them was solved even before his book went to publication.
Just because we don't know something doesn't mean that 'GOD DID IT'.
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