I have noticed the same thing happen with my fleet upgrades and queueing captial ships. I upgraded about 3 tiers of captial fleet caps at once, and then purchased all of my capital ships, but none of them began building until all of my cap fleet upgrades were completed. I have also noticed an issue with logistical slots where it will not allow me to actually begin logistical buildings until the logistical upgrades are completed, whereas with my tatical slots, I can queue tac buildings as soon as I queue up the tac slot required to build it.