When I remove the mirror axes in a 3d plot, pyxplot cuts the output figure to the height of the z axis. This can be checked with the simple script
set axis z nomirror
set axis x nomirror
set axis y nomirror
set nokey
plot 3d sin(x):sin(y) with surface
If I also set the z axis to be invisible, the figure is cut even more.
figure showing the cut of the output when axes are not mirrored.
Thanks for your bug report. I believe this is fixed in svn 1284. apologies this was missed in release 0.9.0... please confirm this is fixed for you.