I've noticed this several times on two different Windows 8 64-bit installations. When I perform a fresh install using the Windows installer, I get the latest build of the binary Chrome extension. The next time the extension auto-updates itself to a new version, however, I find myself with the non-binary extension.
I generally only notice the change when a feature requiring the binary component randomly stops working. Then I check and, sure enough, I'm running a newer version without the binary component. The only way I've discovered to fix it is to download the Windows installer again and re-install.
For a while, I thought I was going crazy, but I just saw it happen again on another machine. Is this the expected behavior?