iBooks disappear when syncing

Ever since I've updated to iOS 8.3 from iOS 7 I've had trouble with iBooks. I have around 3000 books in the iBooks app on my computer and for some reason only about 900 appear on my iPod whenever I try to add more. When I select sync all books, it'll say syncing (blank) books out of like 2000, but it'll stop after adding about 200 or so. Then it'll show up as selected books, but with one less. So then I constantly need to repress sync and it takes a couple hours to do even 1000.

But the main problem is that, say the previous day I've synced on 1000 books in addition to the 900 on the iPod, the next day if I plug in the iPod and say sync all, all the books added the previous day will have disappeared. This happens every time I try to sync my iBooks, about 900 stay on the iPod and nothing happens to them but any other books I add on seem to disappear when I try to sync the rest of my books on. I can't even just put them all on because it would take an entire day (and the books disappear even if I unplug the iPod for like half an hour and then continue to sync) and I would even be able to sync my iPod at all, let alone add new books because just by syncing the books disappear. I don't know why it's happening only on the iPod, my iPad is fine. PLEASE HELP.

The only solution I've found is sending myself my new books by email and opening each one in iBooks, forgoing putting them into iBooks on the computer, but even then when syncing, some will disappear.

Also, I don't know if this is related, but the iBooks app on my iPod always has the loading symbol or whatever in the top right corner, where it normally says select and the first time after syncing when trying the read a book it'll freeze multiple times and I have to close and reopen the app to continue reading the book and it'll forget all progress in the book (meaning if I got to page 20 and its a new book, when I reopen the app it'll open on page 1 or even on the last book I was reading and will be like i didn't even open the new book.)

Any help would be greatly appreciated and thank you so much.