<p>I read a little of the help for my advanced installer 6.5.1 and couldn't find a way to change the version string except by hand.</p>

The files for creating an MSI are usually in XML format, we've created a little tool that runs as part of our build process that goes and changes the build number manually, try openning the advanced installer file in notepad and look for the "ProductVersion" string.
Cheers,
Rob.