Do your iPad's each have their own names? I.E. - My iPad - Her iPad. iTunes should remember the configuration of each iPad when you sync - unless the iPads both have the same name.
After rereading you post - if you have no other problems with your own unique content set up, I assume that they do have different names.
You have selected the exact books in iBooks that you want to sync to each iPad correct. You pick your books by putting the checkmarks next to the names and you sync your iPad and then she selects all of her books the same way and then she syncs? The second person syncing would have to click on Apply in order to change the configuration on their iPad.
Message was edited by: Demo