I'm using Octave 4 and GNUplot 5.0.3. I get a black rectangle in my plots whenever I use "print -deps file.eps" (does not depend on the format). Strangely enough, 3d plots (plot3()) are printable, only 2d plots give a black rectangle. The axes are shown, but not the contents. All plots display perfectly in aquaterm, I just can't save them from a script.
P.S. I tried gnuplot 4.6.6, but that breaks the use of aquaterm for some reason.