Greetings all,
Aside from needing to fix up your query methodology (adopting the use of placeholders "?" would be a good start) you have no else for your if condition. Since there is no else that might be the reason "It's printing all the elements of @id as checked".
try something like this

if ($identifier eq $id[$i]){
  print "<tr><td><input type=\"checkbox\" name=\"rt\" CHECKED value=\"
+$id[$i]\"> $id[$i]</td></tr>";
} else {
  print "<tr><td><input type=\"checkbox\" name=\"rt\" value=\"$id[$i]\
+"> $id[$i]</td></tr>";
}
[download]

HTH
-injunjoel