O-ho! That are MANY systems.
I "solved" the problem for the EA in the game by building just one more mineral storage facility. They immediately begun to build fighters again.
For the Darlok it was sufficient to cancel their treaty with a neutral race to have them build their ships again.
I will have a look into this (especially the Last thing) but your game is so big that it takes forever to make one turn. Furthermore the Darlok use more ship classes then a "normal" race and your game is so big that even this can result in errors (I had a fatal RCE in the ship design menu with your game for example). So I can't pinpoint it exactly but I will have a look into it.