In the end Microsoft settled with Sun, and exited the Java business. In the terms of the agreement, Microsoft will include their older JVM with Windows for several more years, for the convenience of its customers. Sun Java and Microsoft Java can exist together on the one computer - they have no dependance on each other. Sun Java in particular does not interfere with the Windows install. Often they are too general to be of use.
Tips also tend to be subject to opinion.
Mine are no different, so don't necessarily believe everything I say. The following is offered as a place to start looking for problems. Information about what is installed is stored in the registry. It's not perfect, sometimes one piece of software replaces a particular file it needs with a certain version, and this breaks another piece of software that relies on the previous version of that file. You can also buy some third party software that fixes things when they are in conflict, but it's not foolproof - ask at your PC shop.