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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?