Sorry, crap patch. This one may be better:
--- /var/tmp/jython 2013-04-10 17:36:27.000000000 +0100
+++ /usr/bin/jython 2013-04-10 18:33:48.000000000 +0100
@@ -6,11 +6,12 @@
# Released under the GPL.
use strict;
+use File::Basename;
use Text::ParseWords;
# Debian constants.
#
-my $jythonHome = '/usr/share/jython';
+my $jythonHome = dirname(dirname($0));
my $debianJNIDir = '/usr/lib/jni';
my $defaultRuntime = '/usr/bin/java';
@@ -87,7 +88,7 @@
$ENV{CLASSPATH} = $classpath;
# Decide upon the python path.
-my $jythonPath = "/usr/lib/site-python";
+my $jythonPath = "/usr/lib/site-python:/usr/share/jython/Lib";
# Set up the cache directory.
#
