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I attached a scenario file with two Mogami class FFG engage two types of Kongo class with SSM.
Kongo class on left is old Kongo class without SM-3 and right one is new one with SM-3. You can see Kongo class with SM-6(right one) does not fire SM-2 automatically.

Edit
-It is SM-3 not SM-6

In your save, none of the Kongos have SM-6s.

It fires automatically if you remove the SM-3s. The fire control seems to get confused and is trying to fire the SM-3 first. But it can't because the SM-3s can't fire below its minimum engagement height. Delete the SM-3 record or zero out the weapons on the VLS mount and the SM-2s fire away. There is some kind of conflict the WRAs, firing priority, and the fire control on the ship.