Hi, It is mentioned in http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-gnuplot.html#sec-2_1 that there were some problems with gnuplot on Windows machines. I came up with a small fix which makes it possible to use Cygwin version of gnuplot with org-mode. The change is in the org-babel-execute:gnuplot function where I added passing of optional argument to org-babel-process-file-name:
before: (org-babel-process-file-name script-file)))) after: (org-babel-process-file-name script-file t)))) The argument forces the function not to add backslash prior to ":" character which prevented gnuplot from finding the script for execution. I hope somebody will find the fix useful. Unfortunately I don't know if the fix breaks anything on Unix/Linux/Mac. Thanks Alex Vorobiev