Is this about "boxed overlay text style" that is used for things like energy usage of a ship when energy is low or cooldown after move timers of fortresses and mobile space docks, and how they can "jump around" a bit when not zoomed in enough to make the "close" sprites appear?
If so, then I've seen that ever since, well, the switch to the Unity engine.
I've found that if you zoom all the way in to the ship or structure having the issue, wait a bit for everything to load, then the problem is fixed for that unit type even if you zoom back out.
If this "workaround" works for the issue you are describing, then we are likely talking about the same issue.