To
AndyP and everyone having trouble with the pirate spawns:
What I deducted from thorough testing and info from other players, the pirate reinforcement wave can spawn anywhere in the 3x3x3 sector cube with the station in the middle. The problem is, that you don't have vision to all those, you have vision only to 7 sectors out of that 27, because what you see is the sector you're in, and the 6 that share a side with yours. You don't see into sectors situated diagonally to yours. There is only 25.9% chance that the pirate wave spawns in a sector you have vision and sensors coverage in - which is why you usually don't see the pirates: they have spawned in one of those diagonal sectors and the best way to find them is to check the corners of that 3x3x3 sector cube surrounding the pirate station. At least, that seems to work for me. Check the upper corners first as they are more likely to spawn there.
/initiate_wave works because that command always spawns the baddies in the same sector you're in. Station attack triggering pirate spawns used to work the same until the wave customization update. What would certainly solve the matter is making only the 6 sectors adjacent to the pirate station, and the station's sector itself eligible for spawning the pirate wave. Thus, they'd always show up on your nav.