This website lists critical problems that I solved when using Gnuplot.
When I used the epslatex terminal and processed it using LaTeX via the built-in pdfLaTeX compiler, the image for my multiplot (in PDF) was severely cropped. Upon much investigation, I found that the bounding box is incorrect.
To change the bounding box of the eps image, just open it using notepad and find for the key similar to this:
%%BoundingBox: 50 50 407 333
Change the last two numbers to adjust the bounding box of the image. Next, the size in the *.tex file corresponds to the old bounding box. So you'll need to change that value as well:
\begin{picture}(7142.40,6200.20)%
That would solve the problem!