It seems that stopall doesn't work when do start patch.dict to sys.modules.
I show sample scripts the following.

Using stopall test case seems to always refer the first mock foo object.
But using stop it refers a new mock foo object.

$ cat test_sampmod.py
import foo

def myfunc():
    print "myfunc foo=%s" % foo
    return foo
$ cat test_samp.py
import mock
import sys
import unittest


class SampTestCase(unittest.TestCase):
    def setUp(self):
        self.foo_mod = mock.Mock()
        self.m = mock.patch.dict('sys.modules', {'foo': self.foo_mod})
        self.p = self.m.start()
        print "foo_mod=%s" % self.foo_mod
        __import__('test_sampmod')
        self.test_sampmod = sys.modules['test_sampmod']

    def tearDown(self):
        if len(sys.argv) > 1:
            self.m.stop()
            print ">>> stop patch"
        else:
            mock.patch.stopall()
            print ">>> stopall patch"

    def test_samp1(self):
        self.assertEqual(self.foo_mod, self.test_sampmod.myfunc())

    def test_samp2(self):
        self.assertEqual(self.foo_mod, self.test_sampmod.myfunc())

    def test_samp3(self):
        self.assertEqual(self.foo_mod, self.test_sampmod.myfunc())

if __name__ == '__main__':
    suite = unittest.TestSuite()
    suite.addTest(unittest.TestLoader().loadTestsFromTestCase(SampTestCase))
    unittest.TextTestRunner(verbosity=2).run(suite)
$ python test_samp.py stop
test_samp1 (__main__.SampTestCase) ... foo_mod=<Mock id='41504336'>
myfunc foo=<Mock id='41504336'>
>>> stop patch
ok
test_samp2 (__main__.SampTestCase) ... foo_mod=<Mock id='41504464'>
myfunc foo=<Mock id='41504464'>
>>> stop patch
ok
test_samp3 (__main__.SampTestCase) ... foo_mod=<Mock id='41504720'>
myfunc foo=<Mock id='41504720'>
>>> stop patch
ok

----------------------------------------------------------------------
Ran 3 tests in 0.004s

OK
$ python test_samp.py
test_samp1 (__main__.SampTestCase) ... foo_mod=<Mock id='19152464'>
myfunc foo=<Mock id='19152464'>
>>> stopall patch
ok
test_samp2 (__main__.SampTestCase) ... foo_mod=<Mock id='19152592'>
myfunc foo=<Mock id='19152464'>
FAIL
>>> stopall patch
test_samp3 (__main__.SampTestCase) ... foo_mod=<Mock id='19182096'>
myfunc foo=<Mock id='19152464'>
FAIL
>>> stopall patch

======================================================================
FAIL: test_samp2 (__main__.SampTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_samp.py", line 27, in test_samp2
    self.assertEqual(self.foo_mod, self.test_sampmod.myfunc())
AssertionError: <Mock id='19152592'> != <Mock id='19152464'>

======================================================================
FAIL: test_samp3 (__main__.SampTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_samp.py", line 30, in test_samp3
    self.assertEqual(self.foo_mod, self.test_sampmod.myfunc())
AssertionError: <Mock id='19182096'> != <Mock id='19152464'>

----------------------------------------------------------------------
Ran 3 tests in 0.003s

FAILED (failures=2)
$