If you are using iTunes (I presume with iBooks) then what you describe is not the way to do it. What you should do is instead use the "connect to iTunes" option from the Connect/share menu and then use "send to Device" to transfer the books.
You might want to look at the first post in
this thread for more information. Note that although the thread title refers to iPad it now applies to any device running iBooks and transferring the books via iTunes.