I find this line is printed out multiple times:
I even tried an older version of gnuplot (4.2 patchlevel 6). But it does not help.
Commenting out the line 14
<!-- <include ignore_missing="yes" deprecated="yes">~/.fonts.conf</include> -->
solves my problem.
It is marked as
<!-- the following elements will be removed in the future -->. However, I guess I should remove it now to make programs work well again.