iBook highlights sync incorrectly since iPad was restored

About a month ago I was having issues with my iPad and decided to try a total wipe and restore. For the most part, everything went back to normal, but I've been having one issue with iBooks.

The two books I previously purchased through the store (the four-book set from Game of Thrones as well as the fifth book separately) have a large number of highlights and notes. Since restoring, the "NOTES" menu by the table of contents has all the correct information in it, including the actual highlights and any notes that I typed to go with them, however, when I click on the notes, it takes me to the completely wrong page of the book.

For example:

I previosly highlighted the name of one chapter, "Jon." On the NOTES page, it says, "Jon... page 1192." When I tap on the note, it does take me to 1192, but that's the beginning of a totally different chapter. "Jon" actually starts on pg 1154.

In some cases, when I tap on the note, it shows an entire chapter highlighted (not even the right chapter). When that happens, it also tends to freeze until I either go back to the contents page or close the app completely.

I have tried deleting both the books and the app and re-syncing through iTunes as well as re-downloading directly from the store. I have also tried changing the size of the font, as well as the font itself. The highlights work fine with books that I have purchased after the restore, as well as older books I downloaded from Gutenberg.org. I also tried adding a new highlight on one of the books that has a problem ("Jon" on page 1154 from my example above) and the new highlight works fine.

Is there anything else I can try to get these back to normal? Thanks!