Hi - I hope this helps someone.
I set up a new indigo server - using a case sensitive file system.
Strange - after installing the Matplotlib plugin, it was missing its "Configure..." menu entry.
In the "Server Plugin" folder, the file "pluginConfig.xml" did not follow the indigo naming convention of "PluginConfig.xml"
Renaming the file with the capital "P" restored the "Configure..." menu entry after a server restart.
Or the plugin gods granted me a wish for an hour of head banging on keyboard.