Can you post a short code sample that shows this effect?  I have just tested this using:
static void testExtractVector()
{
	std::vector<MyClassScope::MyPublicType>& foo;
	foo.size();  // extract this line only
}
and I ended up with the new function:
void MyMethod( std::vector<MyClassScope.MyPublicType> &foo )
{
	foo.size();
}
I have seen the problem characters, but not for a while.  I know of one bug that will produce then in VA 1544, but this only happens under fairly specific conditions.