I have had a look at the book and a test and I didn't have any problems.
Firstly I loaded the epub as an epub and had a quick look. Not issues.
Then I used Joel's driver to send it as a kepub. Again, no problems. I downloaded the driver yesterday, so it is the latest version.
I also opened both epub and generated kepub in Sigil with no problems. Sigil did object the the property added to the cover in the OPF for the kepub, but that is expected. I also ran epubcheck against both versions with the same result.
I loaded it onto both my Glo and my Touch. I checked the database on both, and there are no problems with them.
I don't know what is happening. It might be something in the version of Joel's driver that you were running. I can see that he has made some changes since then, so maybe he has fixed the problem.
Before trying this book again, could you take a copy of the database. Then, if it messes up the database, take a copy of the corrupt database and send them both to me. I can compare them and maybe see if something else is happening.
Also, I can't see it mentioned above: what firmware version are you on, and how did you get to it? Was the upgrade via the deskopt/WiFi or sideloaded?
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