The problem is that when you copied the books to iBooks (or Books as it is now unaffectionately known), the .zip epub container was unpacked into a directory.
There is a script available on Mobileread in the
ePub Zip/Unzip AppleScript application for Mac OS X thread but I'm not sure if it will still work. I did play with
eCanCrusher a couple of years back and it worked on a virtual Mac.
If you use your favourite search engine for a search such as "OSX script for packing directories into epub files" comes up with quite a few hits.