In what format did you installed it in ? DSP or VST ? Most of these 3rd party plugins get installed in more then one location, being in different format, intended to be used on different applications. If Musicbee can still can scan it, it has to be lingering somewhere. Try finding the .dll in your programs folder as well as the plugins folder of the Musicbee.
Also, if you're looking for a simple, kick-ass plugin to manipulate the audio, try looking for Fabfilter Pro-Q 2.
For surgical uses, this is the most sort out plugin in the audio world because It has unmatched transparency. My entire library is encoded in V0 with lame 3.98.4. which averages out around 245 K/bps With Fabfilter (and some other tweaking) I listen to the synths in the background clearly that wouldn't be possible otherwise unless listening to the lossless compression.