When I export my model from Blender and import it into Unity it has a rotation so when I set the rotation to 0 in Unity it...

The rotation should match what you had in Blender. Make sure that your view in Blender isn't tilted. Use the grid to determine which way is up. Also note the Y axis for your model. In Unity Y is up and down while the Z axis is sometimes used for this on certain models. Ideally this would be fixed in your model itself but you can also use an empty game object as the parent. Here is a more in depth look at this issue: http://docs.unity3d.com/Manual/HOWTO-FixZAxisIsUp.html Note that this SHOULD be fixed when exporting an FBX file from Blender into Unity. While Blender does use the Z axis for up and down, when you bring it into Unity it's "converted" and now uses the Y axis for up and down while keeping the same rotation values as the original.

I think this is some quirk with Unity and Blender. I only have a single object so when importing in to blender it's setting the X rotation as -90. At 3:36 in the video when you go into the individual meshes each one has it's X axis rotation set as -90 which is the same thing I'm experiencing. I've just done a test and added an additional object in to my file and the parent container x rotation is 0 and the child meshes are -90. So it looks like having a empty parent object will do the trick. Thank you for your help!