Please, paste the test source at somewhere.

<?php
class SegfaultTest extends PHPUnit_Framework_TestCase
{
    protected $handler;

    public function setUp()
    {
        try
        {
            $this->handler = new PDO( "sqlite::memory:" );
            $this->handler->sqliteCreateFunction( 'md5', array( 
'ezcQuerySqliteFunctions', 'md5Impl' ), 1 );
        }
        catch ( PDOException $e )
        {
            $this->markTestSkipped(
                'PDO session could not be created: ' . $e->getMessage()
            );
        }
    }

    public function tearDown()
    {
        unset( $this->handler );
    }

    public function testOne()
    {
    }

    public function testTwo()
    {
    }
}

The segfault appears the second time it executes $this->handler-
>sqliteCreateFunction() in the setUp().

If unset() isn't used in tearDown(), then there is no crash.

I have been able to reproduce it without PHPUnit.
I committed ext/pdo_sqlite/tests/bug60104.phpt to make it easier.

Dmitry, could you take a look at it?
Looks like something is wrong with that caching thingie in the executor.. 

(gdb) f 0
#0  ZEND_INIT_METHOD_CALL_SPEC_CV_CONST_HANDLER (execute_data=0x7ffff7f9d1c0) at /local/qa/5_4_valgrind/Zend/zend_vm_execute.h:28949
28949           if ((EX(fbc)->common.fn_flags & ZEND_ACC_STATIC) != 0) {
(gdb) p *execute_data.fbc 
$10 = {type = 90 'Z', common = {type = 90 'Z', function_name = 0x5a5a5a5a5a5a5a5a <Address 0x5a5a5a5a5a5a5a5a out of bounds>, scope = 0x5a5a5a5a5a5a5a5a, 
    fn_flags = 1515870810, prototype = 0x5a5a5a5a5a5a5a5a, num_args = 1515870810, required_num_args = 1515870810, arg_info = 0x5a5a5a5a5a5a5a5a}, 
  op_array = {type = 90 'Z', function_name = 0x5a5a5a5a5a5a5a5a <Address 0x5a5a5a5a5a5a5a5a out of bounds>, scope = 0x5a5a5a5a5a5a5a5a, 
    fn_flags = 1515870810, prototype = 0x5a5a5a5a5a5a5a5a, num_args = 1515870810, required_num_args = 1515870810, arg_info = 0x5a5a5a5a5a5a5a5a, 
    refcount = 0x5a5a5a5a5a5a5a5a, opcodes = 0x5a5a5a5a5a5a5a5a, last = 1515870810, vars = 0x5a5a5a5a5a5a5a5a, last_var = 1515870810, T = 1515870810, 
    brk_cont_array = 0x5a5a5a5a5a5a5a5a, last_brk_cont = 1515870810, try_catch_array = 0x5a5a5a5a5a5a5a5a, last_try_catch = 1515870810, 
    static_variables = 0x5a5a5a5a5a5a5a5a, this_var = 1515870810, filename = 0x5a5a5a5a5a5a5a5a <Address 0x5a5a5a5a5a5a5a5a out of bounds>, 
    line_start = 1515870810, line_end = 1515870810, doc_comment = 0x5a5a5a5a5a5a5a5a <Address 0x5a5a5a5a5a5a5a5a out of bounds>, 
    doc_comment_len = 1515870810, early_binding = 1515870810, literals = 0x5a5a5a5a5a5a5a5a, last_literal = 1515870810, 
    run_time_cache = 0x5a5a5a5a5a5a5a5a, last_cache_slot = 1515870810, reserved = {0x5a5a5a5a5a5a5a5a, 0x5a5a5a5a5a5a5a5a, 0x5a5a5a5a5a5a5a5a, 
      0x5a5a5a5a5a5a5a5a}}, internal_function = {type = 90 'Z', function_name = 0x5a5a5a5a5a5a5a5a <Address 0x5a5a5a5a5a5a5a5a out of bounds>, 
    scope = 0x5a5a5a5a5a5a5a5a, fn_flags = 1515870810, prototype = 0x5a5a5a5a5a5a5a5a, num_args = 1515870810, required_num_args = 1515870810, 
    arg_info = 0x5a5a5a5a5a5a5a5a, handler = 0x5a5a5a5a5a5a5a5a, module = 0x5a5a5a5a5a5a5a5a}}

I would say that the problem in "magic" PDO extension design. It creates and destroys method tables at runtime. See pdo_hash_methods() at pdo_dbh.c. As result ZE can't cache bindings of for such methods.

The problem may be solved in few ways.
1) Fix PDO
2) Introduce additional fn_flag that disables method caching
3) Disable method caching for classes with custom get_method handler

I think (2) is the simplest solution that won't make performance degradation. PDO fix would make it faster and reduce memory usage, but it's much more serious task. I just don't have time to do it myself.

If 2) is implemented right now, could 1) be made for a minor version of 5.4 
without breaking the ABI?

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/.

 For Windows:

http://windows.php.net/snapshots/
 
Thank you for the report, and for helping us make PHP better.