I seem to have a lot of trouble with waves being seen also. I re scan a couple of times, remove the folder in "preferences" to scan that has waves in it, then add it back in. Once I think I re scanned my whole C drive.
It can be scary to have a project with a deadline come back up missing tons of plugins. So you buy a plugin and are dying to see how it does, scan for plugins and instead of having a new plugin....you are missing all your wave plugins. Makes for quite the moment.