tso: I think this is a "feature" of the app manager. If you download and install a deb, then try to overwrite it with a deb from the repos it notices that they have different sources. For some reason it doesn't just alert you and let you have the choice to continue. The easiest way past this is to uninstall your old version and install the new one from the repo.

This isn't a problem after the first install from the repo.