PCBs which render a schematic either with or without jumpers
Thanks a lot for posting the simplified project folder. I was going to ask you to do that. It seems to me that the footprint and symbol must be embedded somehow because I simply opened the project, and from that opened the schematic and pcb file and it all opens OK in 6.0. I get a notice that the file was created by an older version of KiCad etc. but that is not a problem. I am sort of late in responding to your last post and I wanted to thank you for it…but I still need to ponder what you did!! 
OK…This strap which I am looking at has 3 pads. Sorry I guess you said as much. There are two through hole pads connected by one long narrow SMT pad. So really the strap is a long narrow pad. The schematic shows all three pads connected at one point in the schematic.
So now I have brought your strap symbol into the local high school biology lab and dissected it. (I am exaggerating) It was difficult to see what I had so I selected a pin and moved it. Indeed there were two more in the same place. There were three pins superimposed. If anyone else can bale in and help make sense of it, that might be good. I think you have done a Captain Kirk and cheated on the Kobayashi Maru Test! (No I am not really a Trekky but I was desperate for a metaphor.)
One thing…my use of jumpers is an example of how the layout can drive the schematic. The jumper is not planned but rather I find that I need it when doing the 2 sided layout.
Another thing…I observe that your schematic shows the net to which the jumper is connected but might not show which components are on which end. So it is sort of depriving the schematic of some information. Of course, the schematic also does not show tracks per se, and the strap is just a replacement for a track. So maybe that is the important point of all of this.