Modified examples to reproduce the error

Just run these 2 commands
$ examples/program2-no-wrapper.rb # without script
$ examples/program2.rb            # with script

examples/program2-no-wrapper.rb

@@ -0,0 +1,12 @@
+#!/usr/bin/env ruby
+INPUT = 3
+require File.dirname(__FILE__)+'/scripts/script.rb'
+
+# raise if defined?(INPUT)
+
+p OUTPUT
+p MORE_OUTPUT
+
+run
+
+puts "x = #{x}"

examples/scripts/lib/a-class.rb

@@ -0,0 +1,5 @@
+
+module BaseModule
+  class A < BaseClass
+  end
+end

examples/scripts/script.rb

@@ -4,8 +4,15 @@
 
 OUTPUT = ["input was #{INPUT}"]
 
-require 'lib/x-accessor'
-require 'lib/x-accessor' # only loaded once
+module BaseModule
+  class BaseClass
+  end
+end
+
+require File.dirname(__FILE__)+'/lib/a-class'
+
+require File.dirname(__FILE__)+'/lib/x-accessor'
+require File.dirname(__FILE__)+'/lib/x-accessor' # only loaded once
 
 # Falls back to Kernel.load, since "benchmark.rb" isn't in the current dir.
 load "benchmark.rb" unless $LOADED_FEATURES.include?("benchmark.rb")