That's a kinda weird bug. Though I suppose weird bugs is what you get when you keep pushing the envelope of what Nova can do. It might be worth testing whether some or all of this stuff will actually work on the opposite platform before you get too far with it. PC Nova is particularly notorious for breaking on things that Mac Nova can handle fine.
Is the deal with the PD weapons that the higher ID weapon adopts the range of the lower ID weapon, or simply that it does not fire at all until the enemy is within range for the lower ID weapon? That is, does it retain its original range, but does not fire until the ship is in range of all PD weapons on board? It'd be a bit hard to test this if you're still using that invisible PD weapon.
Does the same occur for point defense beams?
On a side note, my questions in your other thread weren't so much for figuring out why the problem was occurring. Rather they were attempts to elicit more information out of you about the behaviour of extremely long-ranged submunitioning weapons, on the off chance that someone else were to try a similar thing.