Error importing csv with batch API
Found the error: the problem is that I'm not resetting $context['sandbox']['file_pointer_position'].
This causes batch pointer start reading the CSV file in the wrong position.
To correct this, it's enough to add  

$context['sandbox']['file_pointer_position'] = 0;


to the check for EOF  

if (feof($file_handle)) {
    // complete the batch process
    $context['sandbox']['file_pointer_position'] = 0;
    $context['finished'] = 1;
    // end loop
    break;
}