I seem to recall that I got weird lags when I had templates enabled across factions. There was some setting that would duplicate some regular building template, say mass storages, so that when you create it as e.g. aeon you'd have the same template for all other factions. I still remember being pissed of having to create them separately for each faction
So I guess there is a chance this would be the culprit as it would be stored in game.prefs file.