Двукратное решение. 1) разница в виду графиков была вызвана ошибкой в 5.2.2. Обновление до 5.2.3 исправлено.
2) Решил проблему с сеткой, построив журнал данных на линейных осях и затем поместив оси в логарифмический вид.
Сюжет необходимо улучшить, сделав меньшие тики меньше основных.
set pm3d
set pm3d map
set cntrparam levels auto
set contour surface
#set xrange [2:6] #setting this makes the image finish at the y2 tics, without changing the xtics
set xtics 2,1,6
unset xtics
# "major" tics
set xtics ("100" 2, "1000" 3, "10000" 4, "100000" 5, "1e6" 6)
# "minor" ticks
set for [i=2:6:1] xtics add ("" log10(2*10**i),"" log10(3*10**i),"" log10(4*10**i),"" log10(5*10**i), "" log10(6*10**i),"" log10(7*10**i),"" log10(8*10**i),"" log10(9*10**i))
set ytics -2,1,-1
unset ytics
set ytics ("0.01" -2, "0.1" -1)
set for [i=-3:0:1] ytics add ("" log10(2*10**i),"" log10(3*10**i),"" log10(4*10**i),"" log10(5*10**i), "" log10(6*10**i),"" log10(7*10**i),"" log10(8*10**i),"" log10(9*10**i))
splot "test_data.dat" using (log10($1)):(log10($2)):3