OK, whatisup. As indicated in the User's Guide, "Copy Newer" and "Copy Different" do not guarantee a bootable result. You have to use either "Smart Update" or "Erase, then copy".
If you Smart Update the drive at this point, it should fix it up so you can once again boot from it. Note, though, that it will also remove any files from the destination that are not present (and selected) on the source.
Hope that helps!
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--Dave Nanian
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