I just had to jump in here I guess...not sure if the OP understands what the targeting problem looks like. I notice it when running 1440x900, as a targeted ship gets closer to the edge of the screen, the targeting box moves more and more off center (towards the outside of the screen.) The OP might not actually be having this problem, but none of the screenshots here that I saw really determined that one way or another. It doesn't bug me really all that much, but does make me wonder if the gun-leading reticle is really in the right place. I am not sure what version I have but I just did the whole online installation thing yesterday.
Otherwise I am pretty pleased with my experience with the game so far. Running an older 2GHz machine, 6600GT card, everything turned all the way up and no problems with framerate or anything.