Can you give any more information about that book? Is it named "Kindle Sabotage" or something like that?
Depending on where you got the book from, complain to the publisher, and maybe also report to Amazon that this book screws up the kindle. As a workaround, try to convert it to epub, then back to mobi, or use some "stranger" intermediate formats like RTF.
It may just be something with the contained html/css, metadata, etc.
Actually, while developing the jailbreak, I managed to (unintentionally) *crash* the Kindle using a few simple CSS commands. All that I tried to do was to center the "==>JAILBREAK<==" text, both horizontally and vertically. Some specific CSS instructions (don't remember what, though) really (consistently, and repeatably) crashed the reader application.
You may be having a similar problem, but affecting (most probably) the indexer.