Your board isn't large enough so the pads are being truncated (I'm not sure why one is only partly truncated as I would expect and the other is completely gone). There will only be board (and thus copper) within the grey area set by the pcb1 part in pcb view. In the sketch below I increased the size of pcb1 to contain both pads completely and then the gerber generates correctly. So you either need to reduce the size of the two pads to fit within the grey board area or increase the size of the board (which may face other constraints such as space 
).
copper pad_fixed.fzz (4.1 KB)
edit:
Here is an alternate with the original board size but the pads moved and reduced in size to mostly fit. I expect the edges outside the grey area will be truncated when the board is made.
copper pad_fixed2.fzz (4.1 KB)
Peter