Apply Scale issues on duplicated object At a loss on this one. I'm sure it's something simple.

I'm currently building a character…. (well nearly finished) the eyes are separate from the main model as I want to move them when animating. 

To try and make it clear I'll explain my workings and then explain the problem. I created an eye using a sphere, and used a lattice modifier to make the eye look flat (as the character is stylised) Before doing the second eye, I textured the model, including the eye. I then duplicated the eye and mirrored it (so that eye is textured too) and did the same for the lattice. Looks great and does exactly what I want it to do. 

This is the problem. When exporting it as an FBX it tells me I need to apply scale. Thats fine. So I apply scale on the main body of the model, and the two eye balls. All seems fine. But, when in object mode and I press "P" on the keyboard, the render tells a different story. The duplicated Eye has done a 180 turn. The first/original eye is fine, so is the body. Before applying scale and pressing "P" the duplicated eye is fine.

I don't understand, for a start, that this only shows up when rendered, and when I put the fbx into the game engine I'm using, it shows the eye rotated (this is how I discovered the problem in the first place.) But looks fine in my 3D window in blender. Also, its only that duplicated eye thats messing up. Is there a way I can apply the scale but keep it as it is.

Any ideas?
From the problem you described. I have a few suggestions.
To "apply the scale but keep it as it is":

On your duplicated eye. Press CtrlA then apply "Rotation &amp; Scale". The reason for rotation is because scale would not make it flip, but rotation might.