OK, I can see what's going on, and have a good idea how it is happening. Objects drawn on the lighting layer should have a fill of transparent, and their fill attribute should be forced to transparent. This is not happening in your case. There is a discrepancy between the behavior of paths on Classic and Jumpgate In Classic , I can draw a polygon with a fill and move it to the lighting layer, where it will retain its fill. New paths drawn on the Lighting layer will be forced to a fill of transparent. on all other layers, an object will default to the fill and stroke of the last selected object. On Jumpgate , The fill of new objects on the lighting layer is not being forced to transparent. It is defaulting to the fill and stroke of the last selected object. At some point you must have drawn an object with a fill of black, and while that was the last selected path, switched to the Lighting layer. The tool did not enforce a switch to a fill of none. This is a bug, in my opinion, and I will report it as such. In the meantime, here is a workaround to fix your current situation. On the lighting Layer, select all of your paths. If you have mixed object types on the lighting layer, you can hold down the alt/opt key while dragging a selection rectangle and that will constrain the selection to only path objects. Right click and send them to another layer, preferably one without any paths. Select them all again on the new layer. The color box will now allow you to set the fill. Set it to transparent, then right click to send them all back to the Lighting layer.