The parameter per_page is left out when the per_page parameter has the same value as declared in the configuration!

in the filter_api.php I found this:
if ( !filter_str_field_is_any( $p_custom_filter[FILTER_SEARCH_ISSUES_PER_PAGE] ) ) {
if ( $p_custom_filter[FILTER_SEARCH_ISSUES_PER_PAGE] != config_get( 'default_limit_view' ) ) {
$t_query[] = filter_encode_field_and_value( FILTER_PROPERTY_ISSUES_PER_PAGE, $p_custom_filter[FILTER_SEARCH_ISSUES_PER_PAGE] );
}
}

Why is that? I left out the second if which give you this:
if ( !filter_str_field_is_any( $p_custom_filter[FILTER_SEARCH_ISSUES_PER_PAGE] ) ) {
$t_query[] = filter_encode_field_and_value( FILTER_PROPERTY_ISSUES_PER_PAGE, $p_custom_filter[FILTER_SEARCH_ISSUES_PER_PAGE] );
}

It is working fine!

In the search page, replace:

$my_filter[FILTER_PROPERTY_ISSUES_PER_PAGE] = gpc_get_int( FILTER_SEARCH_ISSUES_PER_PAGE );

with:

$my_filter[FILTER_PROPERTY_ISSUES_PER_PAGE] = gpc_get_int( FILTER_SEARCH_ISSUES_PER_PAGE, config_get( 'default_limit_view' ) );

and revert your other change.