This occurs due to a bug in php_runkit_function_copy_ctor. There is dupvars initalization for the vars name missing.

Patch is following:

Index: runkit_functions.c
===================================================================
RCS file: /repository/pecl/runkit/runkit_functions.c,v
retrieving revision 1.10
diff -u -r1.10 runkit_functions.c
--- runkit_functions.c	17 Nov 2007 07:40:47 -0000	1.10
+++ runkit_functions.c	27 Dec 2007 17:22:31 -0000
@@ -136,6 +136,8 @@
 	while (i > 0) {
 		i--;
 		dupvars[i].name = estrdup(fe->op_array.vars[i].name);
+		dupvars[i].name_len = fe->op_array.vars[i].name_len;
+		dupvars[i].hash_value = fe->op_array.vars[i].hash_value;
 	}
 	fe->op_array.vars = dupvars;
 #endif
Index: tests/bug10053.phpt
===================================================================
RCS file: tests/bug10053.phpt
diff -N tests/bug10053.phpt
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ tests/bug10053.phpt	27 Dec 2007 17:22:31 -0000
@@ -0,0 +1,65 @@
+--TEST--
+runkit_method_copy() function
+--SKIPIF--
+<?php if(!extension_loaded("runkit") || !RUNKIT_FEATURE_MANIPULATION) print "skip"; ?>
+--INI--
+error_reporting=E_ALL
+display_errors=on
+--FILE--
+<?php
+class runkit_one {
+	private $b = 0;
+	private $c = 1;
+	
+	function runkit_method($naturalNumber) {
+		$delta = $this->c + $naturalNumber;
+		$thisIsAStrangeVariableWithAVeryLongNameHopeThisWillShowTheError = $delta * $delta;
+		$objectVarWithLongName = new stdclass;
+		$objectVarWithLongName->e = $thisIsAStrangeVariableWithAVeryLongNameHopeThisWillShowTheError;
+		echo "Runkit Method: $naturalNumber\n";
+		var_dump($objectVarWithLongName);
+	}
+}
+
+class runkit_two {
+	private $b = 27;
+	private $c = 99;
+
+}
+
+$o = new runkit_one();
+$o->runkit_method(1);
+
+runkit_method_copy('runkit_two','runkit_method','runkit_one');
+
+$o->runkit_method(2);
+
+$o2 = new runkit_two();
+$o2->runkit_method(3);
+runkit_method_remove('runkit_one','runkit_method');
+if (method_exists('runkit_one','runkit_method')) {
+	echo "Runkit Method still exists in Runkit One!\n";
+}
+$o2->runkit_method(4);
+?>
+--EXPECT--
+Runkit Method: 1
+object(stdClass)#2 (1) {
+  ["e"]=>
+  int(4)
+}
+Runkit Method: 2
+object(stdClass)#2 (1) {
+  ["e"]=>
+  int(9)
+}
+Runkit Method: 3
+object(stdClass)#3 (1) {
+  ["e"]=>
+  int(10404)
+}
+Runkit Method: 4
+object(stdClass)#3 (1) {
+  ["e"]=>
+  int(10609)
+}

This bug has been fixed in CVS.

In case this was a documentation problem, the fix will show up at the
end of next Sunday (CET) on pecl.php.net.

In case this was a pecl.php.net website problem, the change will show
up on the website in short time.
 
Thank you for the report, and for helping us make PECL better.