Using the rectangle background with $epslatex seems to hide the axis 
annotations and scales of the figure. I suppose that this is the reason why
 $eps, $epslatex and $epslatex_standalone were treated differently. Except 
that the two lines need to be deactivated.

Using the lisp lines that you pointed out, I modified my gnuplot.lisp in order 
to delete "set obj 1 fc rgb" in ~/maxout. (see patch, lines at 2806,2813)

Best regards
*** gnuplot.lisp_bak	2018-05-18 11:32:33.229304308 +0200
--- gnuplot.lisp	2018-05-18 11:33:43.292520843 +0200
***************
*** 2806,2813 ****
        ; save in plotcmd the gnuplot preamble
        (setf plotcmd
           (concatenate 'string
!             (if *multiplot-is-active*
!                ""
                 (format nil "set obj 1 fc rgb '~a' fs solid 1.0 noborder ~%"
                         (get-option '$background_color))  )
              (if (equal (get-option '$proportional_axes) '$none)
--- 2806,2813 ----
        ; save in plotcmd the gnuplot preamble
        (setf plotcmd
           (concatenate 'string
!             (unless (or *multiplot-is-active*
!                         (member (get-option '$terminal) '($eps $epslatex $epslatex_standalone)))
                 (format nil "set obj 1 fc rgb '~a' fs solid 1.0 noborder ~%"
                         (get-option '$background_color))  )
              (if (equal (get-option '$proportional_axes) '$none)

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