The context menus are defined by XML files stored in C:\Program Files (x86)\Microsoft Configuration Manager\AdminConsole\XmlStorage\Extensions\Actions*GUID* where each GUID corresponds to a unique part of the console. When you install, it copies XML files here. When you upgrade, it should be replacing those files. I wonder if somehow it is not overwriting, and is instead creating duplicates. I’m not sure what exactly would cause the xml duplication, but it would explain two context menus.
Check out the various GUID folders, and see if you can find copies of the XML files. If that is the case, maybe running through an update with logging may give a better idea of what is happening.