I have recently found an issue with alignment in Gnuplot graphs. I have selected simple plot as demonstration - code:
plot sin(x)
set term wxt size 1600,1200 enh
The default format for axis tics is "% h". Note the space in front of the h. I think what your are seeing is that the label is actually " 0" and the placement centers the pair of characters.
set format "%h"
You can change the default format to "%h" instead, but be warned that this may possibly cause other obscure problems due to the program assuming there is always a space preceding an axis label.