Well, they can't be identical because you would have just used the CrTurret03 right? So something must be different,like the factions or AI packages or something. So make a copy of the CrTurret03 and place it in your game. Then go one-by-one and make the changes that turn it into your Turret and check it in game to see which change causes it to stop attacking. Without looking at it, I can only guess, but I'd put my money on some interfaction relationship from the factions you added, perhaps combined with the aggro radius behavior or AI packages. Perhaps placing a little navmesh around the area might help. :shrug:
That's basically what I did. I removed my turret type completely and re-created it with all of the base CrTurret03 options ticked. That turret worked fine, so I then changed its faction to my new faction and - it worked! Given that's what I did in the first place, I have no idea what the problem was, but one thing I have learnt about this GECK is that it is very finicky, so I'm just going to be glad it's actually working and not wonder why!