Hi everyone, interesting thread.
I'm working on a patch that will fix the problem for kindlegen generated files that you're not going to be submitting to KDP.
I've also tested some older versions of kindlegen. This problem of getting two EXTH entries for start of text in the KF8 section of the ebook goes back to the first kindlegen that produced such file: kindlegen 2.0.
So it's a long-standing problem, and while I haven't done a round-trip test myself, I'm willing to believe that Amazon are fixing the problem for books published through KDP.
Note that this doesn't seem to be a bug in the Kindle 3 firmware. It's just that the new Kindle 3.4 firmware is the first that could read the KF8 section, and so is now demonstrating a problem that's been there all along.
Hopefully I'll have a python script and AppleScript wrapper ready for testing something this weekend.