**System Information**
W10 64b
**Blender Version**
2.77a
**Exact steps for others to reproduce the error**
1) {F301309}
2) select all objects
3) File > Export > FBX
4) Check "Selected Objects"
5) Only one cube is exported
It is due to layers, one cube is in the second layers. It start working when you link Scene layer with Render layer (button next to layers button in View3D), you can even turn off it, after you switch on.