Not sure if this is a real problem but it seems like it could be.  I had a bunch of unwanted plugins loaded into the server, and downloaded to my agent.  I disabled, then deleted, then purged many of them in one shot.  

My one agent was running at the time.

Eventually it all settled down and the purged plugins no longer showed up in the gui.  And the server's agent plugins dir showed the correct plugins.

But, on the agent I had one more plugin than expected. The MySQL plugin remained.  This plugin depends on the database plugin. I'd be surprised if it was the only plugin I purged that has a dependency but maybe.  I would think others probably dependended on JMX (basically all of the linux plugins and a few others) but I'm not sure.

I did perform a 'plugins update' prompt command but the plugin remained.  If I were to have a MySQL resource I'm not sure what would happen, it would try to be inventoried but the server would not know about the type.

This was win vista but I doubt that matters.