There's likely some registry keys and files leftover. As a last resort you might try something like Revo uninstaller to uninstall java and FMS before reinstalling FMS, it's important to note that's an opinion, and revo is a program that should not be used lightly.
At this point of time though, it might just be wiser to reformat the box, as multiple install/uninstall/reinstall instances of the same software can turn the windows registry and related directories into scrambled mush.
Thanks for the reply Mike. This was just going to be a test system for me so I'm not feeling a need to reformat or even go the Revo route. Often I find there is some easy fix for something, a trick I didn't know about, so I wanted to check. I'm really not going to miss having to deal with Java so much in 13 Server.