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I am encountering the same issue. My setup also failed at migration 0006. Here is what my auth_user looks like after migration 0005:

                                          Table "public.auth_user"
         Column         |           Type           |                       Modifiers
------------------------+--------------------------+--------------------------------------------------------
 id                     | integer                  | not null default nextval('auth_user_id_seq'::regclass)
 username               | character varying(30)    | not null
 first_name             | character varying(30)    | not null
 last_name              | character varying(30)    | not null
 email                  | character varying(75)    | not null
 password               | character varying(128)   | not null
 is_staff               | boolean                  | not null
 is_active              | boolean                  | not null
 is_superuser           | boolean                  | not null
 last_login             | timestamp with time zone | not null
 date_joined            | timestamp with time zone | not null
 hide_ignored_questions | boolean                  | not null
 gold                   | smallint                 | not null
 email_isvalid          | boolean                  | not null
 email_key              | character varying(32)    |
 date_of_birth          | date                     |
 reputation             | integer                  | not null
 bronze                 | smallint                 | not null
 tag_filter_setting     | character varying(16)    | not null
 last_seen              | timestamp with time zone | not null
 silver                 | smallint                 | not null
 questions_per_page     | smallint                 | not null
 response_count         | integer                  | not null

So, quite a few fields missing (website, about, gravatar)

I took a look at the initial migration - I guess safe_add_column failed silently and continued to the next column.

Edit: I got it to work after manually adding missing columns. I had to add about 7-8 of them each time 'migrate' reached an error. Also had to drop a few tables that were being added multiple times. Isn't this exactly what south is supposed to prevent? Weird.

btw I'm using Django 1.3.1 and PostgreSQL 8.4.11 and integration with an existing project, existing users, and existing auth system (django-allauth).