There is a bug in 4.13.12638 with epubs where the ToC entries reference to anchors in in the text. That bug means that the wrong entry can be selected when the ToC list is opened, and skipping between chapters using the navigation bar can give interesting results. It is discussed in the 4.13.12638 thread. But, I haven't seen any issues with the location or percent read.
What format books are you reading? It could be a format specific problem. Is it every book, or just some? Are any available to download and look at? Or, try a book from the library here at MR and if it has the same problem, we can try it as well.
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