I found the same problem. I built the manhattan project, have chain reactors in most of my cities and have uranium available. I had set 2 cities to build A-bombs, and both were built in the same turn. After that I couldn't build any more and I couldn't build tac-nukes once the appropriate techs were discovered. I even tried using the A-bombs I had (the US Navy took a serious hit in the North Atlantic!) but still was unable to produce any more atomic weapons. I can still build missiles, and nothing pops up when I mouse over the greyed out icon. Any help would be greatly appreciated.
On a side note--anyone know the right f scale integer to make the frigate scale right to the rest of the ships? Having a frigate that is significantly larger than a carrier irks me for some reason...