my @outer;
while (my $rows1 = $query1->fetchrow_hashref()) {
   my $query2 = &db_query("SELECT title FROM pages WHERE sectionid = $sectionid");
   $inner=[]; # you need a NEW array for each loop, not just  an empty array

   while (my $rows2 = $query2->fetchrow_hashref()) {
      push(@$inner,{TITLE=>$rows2->{title});
   }

   push(@outer,{
                 TITLE=>$rows1->{title},
                 PAGES=>$inner;
               });
}
$template->param(sections=>\@outer);