Okay another report of Nephilim, Templar Elite has no engine flare. Also the effect of the weapons platform after they gain the synergy and shield upgrades is mis-aligned and not center with the orb in the center of the platform.
Also when you re-texture the weapon platform may I suggest you texture the orb so that it's more like a central hub where the core power center is. Basically do what you did with the civilian research station, you made the center totally the team color which gave it a awesome effect of making it look like a giant crystal.
Edit: Also I got a mini-dump when I pressed the diplomacy hand icon for missions, by that I mean it was able to open up the menu but when I clicked a faction the game dumped on me. Hope this helps narrow down that issue.