There's no mineral shortages, I can assure you. I've been letting my Duranium accumulate and I've got plenty of Mercassium. Wealth and work force is not a problem. The message says "Fuel Shortage in Production of Research Lab on Earth" and I've gotten it not just once, but twice.
I'm fairly certain this only happens when I complete a ship. When ships refuel on orders and empty the reserve that way, I don't get the message.
I can upload a copy of the log in txt format. In fact, I've already done so on my own web space, but I can't share the url. My young account and post count most likely. I am willing to provide it through any means available.
EDIT: It just happened again. Another ship completed and it reported "Fuel Shortage in Production of Fuel Refinery on Earth". I've got enough Duranium, though I'm running out so I'm not producing as many refineries as I'd like. I haven't hit a shortage yet though. Still 217 in the stockpile and plenty pouring in via mass driver.