I am having the invisible ship problem too, except all my ships are invisible, including factories etc. and it's happens on all the maps I have tried, including non random ones, even in the tutorials I have everything invisible.
And when I start up I get this error:
Failed to Create D3DX Effect '.\PipelineEffect\GS_Ship.fx'...
.\PipelineEffect\GS_Ship.fx(257,7): error X3000: syntax error: unexpected token '='
Skip,
Failed to Create D3DX Effect '.\PipelineEffect\GS_ShipBuilding.fx'...
.\PipelineEffect\GS_ShipBuilding.fx(234,6): error X3000: syntax error: unexpected token ';'
Skip.
What can I do to bring the ships back?
Try these 3 steps:
1. If your using vista try running the game with admin rights.
2. update your directx
Link3. and last one, try reinstalling the game
hope it helps

The invisible ship problem is known and fixed. Nothing the user can do but wait for a patch