Views pager uses wrong URL when using views_embed_view()
Manually set $_GET['q'] to the appropriate value before calling views_get_view().

Views' pager uses the standard Drupal pager from includes/pager.inc which uses this request variable:

function theme_pager_link($variables) {
  // (... code omitted here ...)

  // @todo l() cannot be used here, since it adds an 'active' class based on the                                       
  //   path only (which is always the current path for pager links). Apparently,                                       
  //   none of the pager links is active at any time - but it should still be                                          
  //   possible to use l() here.                                                                                       
  // @see http://drupal.org/node/1410574                                                                               
  $attributes['href'] = url($_GET['q'], array('query' =&gt; $query));                                                     
  return '&lt;a' . drupal_attributes($attributes) . '&gt;' . check_plain($text) . '&lt;/a&gt;';   
}