I expected I would be able to research the next two fleet upgrades and queue the factories to build the ships. I thought as the fleet upgrades became available, ships would begin to build. What I had was 64 HC queued to build (10 fleet supply each) and 2 fleet upgrades researching. Each upgrade would add 320 fleet supply. My fleet supply was a negative 640. But when the first upgrade was researched then the fleet supply became -320. I expected at least some ships would begin to build since not all of the queued ships were "in the red" However no ships would build until the fleet supply was not a red negative number. They would begin to build if I removed enough queued builds to make fleet supply  0. So all factories are shutdown when you have a negative fleet supply even though you may have enough supply to cover some of the builds.

Easy enough to work around. A rare occurance that anyone would research 2 fleet upgrades at the same time. I thought it interesting enough to mention but if Ironclad never fixed it that would be fine with me. I just thought they might like to know.

Good to know. If you get into a battle while researching a fleet upgrade. Don't get into a negative fleet supply if you want your ships to get replaced.