I've been messing around with the TEC, and I posted my findings on another thread: https://forums.sinsofasolarempire.com/333189
Basicly, the glowing thing switches with another particle effect, and it doesn't just have to be one of the exhaust plumes. I've also gotten one of those little flashing lights to appear in the center. Everytime you build a new starbase, or upgrad an existing one, the effects on all the others ones flip-flop. If the glowing thing was on the side, it usually goes back to the correct place, and if it was in the correct place, it moves to the side. It also happens with the glowing thing on the Vasari SB, but that seems to happen less often. And the other effects on the starbase move, not just the glowing square. Sometimes the exhuast plumes are on the ends of the trade "spikes" sometimes they are on the sides, and sometimes they are where the ship-building orange-glowing exhuast stuff in on the sides.
And the twitching thing happens with the Advent base, too.