The first thing I see is that on Fritzing 0.93b on Win with the latest parts updates, is that there are 3 outdated parts that it wants to update. Letting it update them (it actually updated 13 not 3 as well) doesn't fix the problem and may have broken other things. So I then exported the node cpu part and made a test sketch with it and a 2 pin connector and that tells me the part is broken because the gerber shows the same thing (a trace connected in Fritzing doesn't connect to the pad in the gerber). That is actually good news because I can probably fix up the part for you. Thats good news because it indicates you may not have database corruption (which would require scrapping the entire sketch and starting again which unfortunatly may still happen). I'll have a poke at the part and see what happens.
Peter