I have been able to replicate this a few times, so I wanted to see if anyone else has the same issue:
I open a book on my BlackBerry and start reading it. I stop at Chapter 2, press the Back button and end up at the home screen. Later, I open the book again on my BlackBerry, read to chapter 3, press the back button, going back to the home screen, then exit. So far, no problems.
Later, I go to my Kindle and turn on the radio. The Kindle synchronizes to chapter 3 and I read to chapter 4. I turn the radio back on before going back to the home screen on the Kindle and it syncs the new location back to Amazon. So far, no problems.
I open the ebook again on my BlackBerry. It synchronizes with amazon and opens up to chapter 4 (like it is supposed to). I read to chapter 5. When I press the back button, instead of going back to the home screen, it jumps back to the beginning of chapter 4.

I can go back to the home screen from the menu option as a workaround. If the ebook doesn't have to change locations via synchronization, it goes back to the home screen properly. It's only when the app has to synchronize to a new location first that I see this issue.
I did report it to Amazon. Anyone else with the Kindle for BlackBerry app had this happen?