No, what I mean is: Does your model also look inconsistent in the view in Blender itself (with some faces being hidden when they are not supposed to) when enabling that option.
Enabling this option has nothing to do with how the faces will be exported.
It is only an option for viewing the model, like when you import it and then render the model in your own OpenGL application yourself with backface culling enabled.
Also what is interesting is that Blender seems to generate the winding order depending on the direction of the normal of a face. So maybe check your normals.