Ok, this happens only in missions, space and ground. Sector space and space stations don't seem to be affected. I already did a filecheck within the launcher. Launching the game in Safe mode had no effect on the problem.
Now to my problem. The game ran fine for a few weeks, but now my effects are broken. They are invisible or some blocky noise. I tried lowest video settings without effect. Other games still run fine. Only Star Trek Online has problems.