I could produce this behavior with the binary package gp444win32.zip and with gnuplot 4.4.4 of the Gentoo Linux distribution.
Since I updated to the new version the plot seems to be always shifted to the left.
If I use only ylabel and ylabel2 the automatic right margin is larger than the automatic left margin.
The following code generates the attached PDF which demonstrates the problem:
set terminal pdf color enhanced size 5in,3in
set output "test.pdf"
set style data lines
set ylabel "test"
set y2label "test"
plot sin(x)
set output
example
There seem to be many opinions on the "correct" margin sizes. It is true that the margin placement is different in 4.4.4 than in some earlier versions. Here is the entry in the ChangeLog:
* src/graphics.c (boundary): Tweak auto-placement of plot borders so
that it is closer to what was used prior to version 4.2.4. This makes
the left margin narrower than in 4.2.4 - 4.4.0, and the right margin
slightly wider.
The primary concern is that sufficient room is allowed for axis tick labels, plot labels, timestamps, colorbox with it's own labels, and so on.
I agree that there are many opinions on correct margin sizes.
But i think that when I simply use ylabel and y2labe without anything else it should be symmetric but it is not.
I would suggest to reduce the rmargin when y2label is set.