"Do the ships appear if you save and reload?
What specific ships are disapearing? Debug.err should list what ship models that it can't find."
In my case, they do reappear if I save and reload.
So far I've only seen it in a new game.
The project data window was fine. When in orbit, the 'invisible' ship was represented by a box with nothing but black in it (background?) in the ship list at the right of the screen. By double clicking on it I could get the ship to leave orbit. The ship would be selected and could be moved, but was completely invisible (the blue halo surrounded it showing that it was selected, but there was nothing there). However, if I selected a different ship and then went back to the invisible ship I could not select it by clicking where I knew it was. I could only select it again by finding it in the ship list screen (again, represented by a empty black box) and clicking on that.
I posted the messages from my debug file in the bug thread at the top of the page.