Prova questo:

Codice PHP:
$chiusura_mattino="01:09:00";
list(
$More$Mmin$Msec) =explode(":",$chiusura_mattino);

$chiusura_pomeriggio="00:12:00"
list(
$Pore$Pmin$Psec) = explode(":",$chiusura_pomeriggio);

$ap_eff mktime($More,$Mmin,$Msec,1,1,2000) - mktime($Pore,$Pmin,$Psec,1,1,2000);

echo 
date("H:i"mktime("$ap_eff60"$ap_eff60,0,1,1,2000)); 
in pratica ho ricostruito un timestamp valido.