Pager not working

Trying to output the results of a query to a view and I can't seem to get the pager function to work. I have tried to use both views_theme() and views_build_view.
Background
I have two nodes, Company and Program joined by a Node Reference (Company Name). One company has many programs. I am running a query:
$sql ="SELECT *
FROM `content_type_programs`
Where $where_clause_final
Group by field_program_name_value" ;

then I pass the results to items array:

$items = array();
while ($item = db_fetch_object($query_result)) {
$items[] = $item;
}

Then I am outputting the view:

$view = views_get_view('cost2');
$view->build_type = 'page';
$view->type = 'page';
$view->num_rows = 3;
$view->use_pager;
$view->limit = 2;

views_sanitize_view($view);
return views_theme('views_view', $view, 'block', $items, NULL, array());

I get the desired results BUT I can't seem to get the pager function in the view to work, I always get all the results on one page.
I also tried:
print (views_build_view('embed', $view1, $current_view->args, false, false)); and wrapped this inside the db_fetch_object() loop.

Here is an export of my view:
$view = new stdClass();
$view->name = 'cost2';
$view->description = 'List a Gap Year Company with its corresponding programs';
$view->access = array (
0 => '1',
1 => '2',
2 => '3',
);
$view->view_args_php = '';
$view->page = FALSE;
$view->page_title = 'Gap Company and it\'s Programs';
$view->page_header = '';
$view->page_header_format = '1';
$view->page_footer = '';
$view->page_footer_format = '1';
$view->page_empty = 'Sorry, no results found.';
$view->page_empty_format = '1';
$view->page_type = 'teaser';
$view->url = 'cost3';
$view->use_pager = TRUE;
$view->nodes_per_page = '5';
$view->sort = array (
);
$view->argument = array (
array (
'type' => 'nid',
'argdefault' => '1',
'title' => '',
'options' => '0',
'wildcard' => '',
'wildcard_substitution' => '',
),
);
$view->field = array (
);
$view->filter = array (
array (
'tablename' => 'node_data_field_company_name',
'field' => 'field_company_name_value_like',
'operator' => 'word',
'options' => '',
'value' => '',
),
);
$view->exposed_filter = array (
array (
'tablename' => 'node_data_field_company_name',
'field' => 'field_company_name_value_like',
'label' => '',
'optional' => '0',
'is_default' => '0',
'operator' => '0',
'single' => '0',
),
);
$view->requires = array(node_data_field_company_name);
$views[$view->name] = $view;

I have played around with the view, and the functions views_theme() and views_build_view() for hours but to no avail. Any help would be appreciated. I may be forced to write my own pager in the query if I can't get it to work. Wonder if it has anything to do with the tables being joined by a Node Reference ?????