Regarding Auto-fire. Have you set you skill tray to Type 4? I have found a bug where you cannot activate auto-fire in that tray type and we'll get that taken care of.
If that is the case, try switching to type 3 and activating it from the Ship Weapons instead of the big tray and see if that works. Then you can jump back to Type 4 and continue auto-firing.
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i also noticed that glitched Auto Attack Torpedoes now disappear.
you know, when you turn and are just on the edge of the firing arc a torpedo fires, you turn a little more and another torpedo fires which is the real torpedo (because of LATENCY).
Pre S7 these fake Torpedoes did travel to their target and explode just fine, without doing any actual yellow number damage, but it LOOKED right!
Now they start flying, stay for 2 or 3 km and then disappear from one frame to the next -> looks just wrong.