That's why I said upload it, because I bet the GNDs are labeled correctly in SCH.
Sorry I was wrong about them not turning yellow after ground fill, because I just checked and they still do turn yellow when 1 pin is clicked.
Download this one and try, and then add ground fill and try.
schematic v0.3.5.fzz
https://github.com/noisymime/speeduino/blob/master/reference/hardware/v0.3/schematic%20v0.3.5.fzz
You can test the Gerber with Gerbv - a free program - or an online one
http://gerblook.org/pcb/TDDAmLYGorUtXnieQ3GwCH