https://github.com/screeps/engine/commit/91c9bf03a13743d3837b082f26b0a7689021237d

To sum it up - Active structures are determined by range to the controller. But ties aren't broken consistently.  Extensions (and other structures probably) in re-claimed rooms are messed up.  I'm getting 4 different sets of information.

1. Visual - Some extensions look normal, some are red (duh).

2. Structure.isActive() - One of the red extensions returns TRUE. One of the normal extensions returns FALSE.

3. Room.energyAvailable - The number agrees with what I see visually (not from isActive() )

4. Spawn.createCreep() - This will pull energy from extensions that are visually (#1) marked as active, rather than checking isActive().

What causes the issue?

I think isActive() is based on range to the controller. Ties aren't resolved consistently.

Why is this an issue? 

When I'm re-claiming a room, I inherit the extensions. To keep my extension fillers focused, I filter the extensions based in isActive().... So yeah, the room never fills up, and my spawn process gets choked up.

How'd I resolve it?

Well, on my end - I kept deleting extensions until the problematic extensions were on a path frequented often, so they got filled up in passing.  Not totally ideal.

Thanks! Hopefully someone better at this than me can take a look!

Dewey

p.s. I started deleting extensions soon after this: https://screeps.com/a/#!/history/W59N46?t=19734400

Currently marked normal, but isActive() == false: 5927f47427ccaf9c36aae085

Currently marked red,but isActive() == true: 5925da43966ccf98054823e9