I am experiencing this problem too. There is no posted guidance that I can find. This thread was started in September and here it is almost November and there is no guidance, advice, or reassurance from Cryptic.

I really want to write a few more Foundry Missions, but if they are not going to end properly, what is the use?

Is anyone paying attention to the Foundry and its issues - or is it just a bugged system that will never be fixed?