Version issues with automatic uninstall/upgrade

I can't seem to figure out how to version my product so that an upgrade goes smoothly.

Maybe someone here can give me the small detail I'm missing.

I have a application currently in development and I am frequently updating several machines for testing. I use an MSI installer to do the installation.

The following is true:
1. DetectNewerInstalledVersion = True
2. RemovePreviousVersions = True

I am incrementing my version number (currently at 1.0.0.49). Sometimes, when I rebuild the MSI and try to install, everything works fine. Sometimes, it "works", but the new code hasn't been installed, so although the installation went through, it actually didn't. And sometimes I get the notification that "This software is already installed. If you want to do anything about it, you must uninstall through the Control Panel."

Does it matter whether I use "Build" or "Rebuild"?
What's the difference there?
Am I missing something basic?

Thanks!