When you modify the metadata using Windows MobiPocket Reader the changes go into the .mbp file. What you need to do is get the metadata changed in the original .prc or .mobi file. The
Mobiperl command mobi2mobi will do this, and it even has an option to use your changed .mbp files to get the new info. Note that you don't need Perl to run the "binary" version under Windows, and there is a separate GUI (
Mobi2Mobi v0.13 - GUI for Mobiperl tools).