The Windows builds of the game come with a bundled version of Java that the game uses, so probably not that.
Sometimes I get issues with several Java games/apps where the framerate will just be really bad for unknown reasons - rebooting usually clears it up at least for me.
Do you notice it happening consistently after reloading the game? Just in a particular area near your base or everywhere in the map? Is there a lot of base modules in that one location perhaps?