PDF list on ipad is wrong when viewed through itunes on iMac

I have changed all the pdf tiles within iBooks on my Mac to match how they are named on my iPad. I've viewed them on both platforms and matched them item for item.  When I attached my iPad to my iMac last night to sync it and get updated apps, I clicked on the iPad icon on the left sidebar and then on books, listed across the top which opens ibooks, it says.  The pdf lists that comes up there is NOT the same as the one that show the books listed in iBooks.  I took one of the titles that shows up in the inaccurate list on my iPad while it is plugged into itunes and did a search for it on both my iMac and my iPad and it does not come up on either platform. 
Does anyone know where the info lives that shows up in books when you have your ipad connected to itunes and have clicked on the ipad in the left column and then books across the top?  It is not the list as it shows up in iBooks on the iMac so I have NO idea where it lives.
Also, this is a hard topic to post about because some say it is an iPad issue and some say it is an iMac issue. 
Michelle

Hi sberman,
yes, I have show sidebar selected
I am running 10.9.1 for my OS and  itunes 11.1.5  and I think it is current.  I update usually within a week of new OS as I like to wait and see if the new update settles in nicely before jumping in.
I do have 7.0.4 on my ipad.  I have not run the new update as I am uncertain what will happen with my ibooks items.  As I mentioned in my OP, I have the itmes named the same on my iPad and in my list on the iMac in the library.  When I open itunes to do and update and sync, the list of books in the iTunes window when I select books is NOT what shows in ibooks itself.  So I've held off on the ipad update.
Thank you for taking the time to reply.
Michelle

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