I've seen this happen with some of my models too, in blender select those polygons that are getting flipped in oolite and triangulate them, do this inside blender rather than letting the obj2dat script try and do it, as it looks like the script is getting a bit confused and flipping the normals so that they point into the object rather than outwards.
What might be causing it in your ship model is two verticies really close (or even on top of each other), check that area to see if when you select what looks like one vertex, the current selection info is showing that you have actually got two or more verticies selected, if so try and 'weld' or 'merge' them together.
there's a post here that explains how to weld verticies http://blenderartists.org/forum/showthr ... tolerances
Try not to have too many 'ngons' in your final .obj object that you send to the script ('ngons' is a generic term for any polygon that has 5 or more verticies in it), save out a version in which you try and get everything down to mainly 3 and 4 point polygons (blender may have some selection options that lets you quickly select all polygons with more that 4 verticies, once you have these selected triangulate them, then check the edges are flowing properly, and if not, select then spin them like we saw in the other thread)
edit: i saw this written on a forum "In a BMesh Build, you can select Ngons by going to Select in the 3D View header, picking "By Number of Verts" from the list, and in the Tool Pane (or the F6 menu) picking "greater than" for the Type and 4 in the Number of Verts."
I don't have Blender installed so i'm not sure if that's right, but it may help get you on the right path to hunting down and triangulating your ngons!
Nice ship design by the way, hope you get these issues fixed as it'll look great in game!