What's going on when you get new ships, hit the green arrow, and only some of icons disappear

I playing first game of TA.  I have the menu set so that all ships including colonies are automatically launched.

Later in the game, at the beginning of the turn, I get a bunch of blue icons indicating new ships.  I hit the green arrow.  Normally that means all of the blue icons should disappear.  I hit it and maybe half disappear.  I have found a few ships have not been launched.  Not sure if there is a connection.