Loireag Cloning Does Not Work In A Custom Civilization

I created a custom civilization and selected the Command Ship set that included the Loireag.  When I clicked on the icon to clone the Loireag, I lost the 3 Promethion, but I did not get the Loireag clone.

I am also not getting the special ships like the Ysengard, Nail, etc. when a window appears saying that the ship should be available in my shipyards.  This is a serious downside to the interesting option of creating your own civilization.

I am playing a new game using version 1.00.343803a.