neato -v -Gsize=40,40! -Tpng:cairo -n2 junk1.gv > /tmp/1.png
does not show the picture at all.
neato -v -Gsize=40,40! -Tpng:gd -n2 junk1.gv > /tmp/1.png
shows the picture, but is not useful as the font is bad, among other things.
Are you able to repeat this? Fixable?
Input file: b2097.gv
Output file: b2097a.png
If the coordinates are changed to make the drawing a tad smaller, the image re-appears. I'm guessing that cairo or our plugin must assume the scaled down image is too small and optimizes it out.
I found a temp fix: just scale the image file to a small size (say 60x60 instead of 400x400). Seem that the compression down to small size is one reason why cairo failed.