The last component you just make is not on a single plane. those component you just created is at a curved surface. if You unhide the hidden geometry you will see your problem (to unhide hidden geometry go View -> Hidden Geometry) .

My suggestion is create the component that on a single plane. Remove the two windows that isn't on the plane with the door. Then place them on their place. But There is a different size of area after you place the door, so you cant just put the windows next to them.

Link for SKP file of the image above http://pangeranberbajuputih.deviantart.com/art/G-12-Explorer-1st-skp-170076777

Software Use:
Google SketchUp7
plugins use
-Weld
-Extrutions Tools(Etrude Edges By Rails)
-FredoScale

This Is the basic design for my space ship.
This is a luxury civilian space ship. The shape is inspired by a high speed ferry. it has 4 floor.

The work above is just a quick sketch for higher poly work I'm working now here is the sneak peak

Right now i,m working on the cockpit and having trouble placing door and decorating interior.
but the most troubling thing is that I think I just run out of poly.
Update 1