I can't reproduce this problem using either the [really old] version 4.2.3 or 
current 4.4.0
Gnuplot reports an error message about empty data ranges, but recovers 
gracefully.
Admittedly I'm not running Ubuntu. I tested both 32-bit and 64-bit Mandriva.

Can you get a useful trace of the failure from inside gdb (with line numbers, 
etc)
or from valgrind?

[19] make tstdat ; ./tstdat ; gnuplot_4.2.3

        G N U P L O T
        Version 4.2 patchlevel 3
        last modified Mar 2008
        System: Linux 2.6.31.12-desktop-3mnb

        Copyright (C) 1986 - 1993, 1998, 2004, 2007, 2008
        Thomas Williams, Colin Kelley and many others

        Type `help` to access the on-line reference manual.
        The gnuplot FAQ is available from http://www.gnuplot.info/faq/

        Send bug reports and suggestions to
<http://sourceforge.net/projects/gnuplot>


Terminal type set to 'wxt'
gnuplot> plot 'tst.dat' binary format='%*double%*double" using 1:2
Warning: empty x range [0:0], adjusting to [-1:1]

   sfeam (gnuplot developer)

-- 
gnuplot crashes when binary format ignores all data
https://bugs.launchpad.net/bugs/369671
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