Sorry for the late response! That is... really weird. I've never heard of such a thing. I'm not sure what a silent failure like that would indicate. Have you tried uninstalling the old version and then installing the new version?
When I first installed the new version, I put it in the same directory as the old version to overwrite it, so any problems arising from that should have been undone when I uninstalled the new version or installed it in the other folder. My add/remove programs setting also didn't have a separate listing for the old version when I went to uninstall them.