Hmm well your zip file worked for me - with the one exception that I renamed the files from
table (copy).data table (copy).gnu
I just unzipped it in a new dir, then cd'ed there and started interactive gnuplot, then loaded the .gnu file
I got a nice plot of 'Kinetic energy' versus 'Velocity'
G N U P L O T
Version 4.4 patchlevel 3
last modified March 2011
System: Linux 3.2.0-33-generic-pae
Copyright (C) 1986-1993, 1998, 2004, 2007-2010
Thomas Williams, Colin Kelley and many others
gnuplot home: http://www.gnuplot.info
faq, bugs, etc: type "help seeking-assistance"
immediate help: type "help"
plot window: hit 'h'
Terminal type set to 'wxt'
gnuplot> load "table.gnu"
Like drmgd above I don't understand what your makefile has to do with gnuplot