G-Code doesn't indicate a layer change
MatterSlice adds comments to the G-Code designating every layer, like this:
The Layer View uses these comments to determine what each layer is. Other slice engines do not add these comments to the G-Code, so instead the layer view takes a more naive approach. It recognizes every change in the Z coordinate as a different layer. This approach falls apart under certain circumstances. For instance, if you have Z Lift enabled, the Z axis will move up and down every time there is a retraction. This causes the layer view to recognize these areas as separate layers, even though that is not actually the case.
With Slic3r, you can get it to add the same comments that MatterSlice does by putting the following line in the custom Layer Change G-Code (Settings > Printer > Custom G-Code > Layer Change G-Code).
With CuraEngine, there is no such option. You will simply have to live with the fact that the Layer View is not representing things accurately, and trust that the G-Code will do the right thing. You can also use another program to visualize the G-Code, like gcode.ws.
Sourced from our forums: http://forums.matterhackers.com/topic/106/can-i-add-slicing-engine/7