I think I'm having the same problem. It's useful to keep in mind that the missiles have a "serpentine" programmable block that causes them to circle towards their target instead of flying straight. That said, my missiles always seem to just launch out of the system and continue in that initial launch direction instead of veering towards the target at some point. I solved a few issues by making sure there was excess power, and if you're in creative mode you'll have to change the ownership of all the blocks to "Nobody" because otherwise the merge blocks in the newly built missiles won't stick, so you'll just end up with a bunch of slowly floating merge blocks instead of missiles. but I've tried a number of things and haven't solved the aiming issue yet.

So I turned off the Serpentine programmable blocks, and turned off all the overides on the gyroscopes and they seem to track now. After those changes the missile couldn't course correct enough to hit a target at 1km, but it worked nicely at 2km.