Ah! right you are, when I right clicked on the dots I indeed got an svg. Its possible we have been just missing what it does with svg files all this time. Learned something new again! With the svg in hand (or at least in Inkscape) I see copper0 is in the wrong place. g4465 has copper0 under it and copper1 is under g4455 and you have duplicate pads (you only need one set with the proper grouping). To fix it in xml editor click on g4465 and hit delete. That will delete everything under g4465 including copper1 and all the extra circles. Now if you click on g4454 in xml editor and change its Id to copper1 and set you will have the correct copper configuration and it should now work. Your silkscreen looks to be correct now, (if you like you could do an ungroup after selecting g4476 to move silkscreen to root with the coppers, but it should still work as is just fine). With copper0 as a subgroup of copper1 Fritzing knows to copy the connectors to both copper0 and copper1 in the same position so you don't have to worry about getting both pads properly aligned. You may want to change the stroke:#ffffff in the style command for the silkscreen lines (which is the old standard of white, which doesn't show up in Inkscape to #000000 (black) which is the new standard and shows up in Inkscape. That should do it.