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thanks for reporting this issue. 

i was able to reproduce this and here is the back trace

current thread: t@1
  [1] permute_ip(0x8c6fa70, 0x0, 0x8046588, 0xfeeec5ea), at 0xfeeeca3e
  [2] des_LTX__mcrypt_encrypt(0x0, 0x8c6fa70, 0x0, 0xfeef00b2), at 0xfeeec603
  [3] ecb_LTX__mcrypt(0x0, 0x8c6fa70, 0x8, 0x8, 0x0, 0xfeeec5dc, 0xfeeec7dc, 0xfeee6732), at 0xfeef0153
  [4] mcrypt(0x8dfcd20, 0x0, 0x8c6fa70, 0x8, 0x8046678), at 0xfeee676f
=>[5] mcrypt_generic(0x8dfcd20, 0x8c6fa70, 0x8), at 0xfeee50a0
  [6] zif_mcrypt_generic(ht = 2, return_value = 0x8c6f938, return_value_ptr = (nil), this_ptr = (nil), return_value_used = 1), line 682 in "mcrypt.c"
  [7] zend_do_fcall_common_helper_SPEC(execute_data = 0x8dfcf60), line 313 in "zend_vm_execute.h"
  [8] ZEND_DO_FCALL_SPEC_CONST_HANDLER(execute_data = 0x8dfcf60), line 1602 in "zend_vm_execute.h"
  [9] execute(op_array = 0x8c6f098), line 104 in "zend_vm_execute.h"
  [10] zend_execute_scripts(type = 8, retval = (nil), file_count = 3, ... = (nil), ...), line 1188 in "zend.c"
  [11] php_execute_script(primary_file = 0x8047140), line 2214 in "main.c"
  [12] main(argc = 2, argv = 0x80471bc), line 1190 in "php_cli.c"

here is why this issue is happening

when mcrypt_generic_deinit is invoked , we should set init = 0 so that next request of mcrypt_generic will force user to invoke generic_init again.

here is a patch that can address this bug
[sriramn@sriramn]'PHP_5_3'>svn diff
Index: ext/mcrypt/mcrypt.c
===================================================================
--- ext/mcrypt/mcrypt.c (revision 289068)
+++ ext/mcrypt/mcrypt.c (working copy)
@@ -780,6 +780,7 @@
                php_error_docref(NULL TSRMLS_CC, E_WARNING, "Could not terminate encryption specifier");
                RETURN_FALSE
        }
+       pm->init = 0;
        RETURN_TRUE
 }
 /* }}} */

This bug has been fixed in SVN.

Snapshots of the sources are packaged every three hours; this change
will be in the next snapshot. You can grab the snapshot at
http://snaps.php.net/.
 
Thank you for the report, and for helping us make PHP better.