The way the update works is that each component - start menu, Classic Explorer, etc, checks itself if there is a new version based on its own version. Then it launches the Update component to show the dialog. In your case Classic Explorer was version 4.1.0 but the Update was 4.2.4. That's why you get the popup (from Classic Explorer), but then the Update says everything is fine.
I don't know how this can happen. I have not seen reports of this before. If you didn't use the official uninstaller to remove 4.1.0, but something like Revo, it may have left traces of it on the system. Don't do that

Either uninstall from the Programs and Features page, or with the Remove button in the Classic Shell installer, or if all else fails, force-remove it with the Classic Shell Utility.
Do you recall anything out of the ordinary during the upgrade from 4.1.0 to 4.2.4?