I can't believe it! I found 2: 348

 Code:
Your solution passed all tests

KiXtart
KiXtart Version  = 4.60
KiXGolf Script   = kixgolf_ls.kix

Computer
OS               = Windows Vista Business Edition
CPU              =               Intel(R) Pentium(R) D CPU 3.20GHz
Speed            = 3200 MHz
Memory           = 2046 MB

KiXGolf Scoring Engine
Scoring Engine   = 3.3

KiXtart Golf Score
Tournament       = Latin Squares
Processing Start = 2009/01/05 09:48:23.552
Processing End   = 2009/01/05 09:48:23.725
Duration         = 0000/00/00 00:00:00.172
KiXGolf Score    = 348

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 Code:
Function S($o)
  Dim $i, $, $k, $t, $x, $v
  
  For $x = 0 to 16
    ReDim $r[3], $c[3], $q[3], $s[3, 3, $x]
    
    For $ = 0 to 7
      For $i = 0 to 3
        $v = $o[$ mod 4, $i]
        If $ < 4
          $k = 3-2*($<2)-($i<2)
          $r[$i] = $r[$i] + $v
          $c[$] = $c[$] + $v
          $q[$k] = $q[$k] + $v
          $s[$, $i, $x] = $v
        Else
;          If 0 = InStr(Join($r),x)
          If 0 > AScan($r,x,,,1)
            Exit
          Else
            $k = @
            For $t = 1 to 4
              If 0 = InStr($c[$-4]+$r[$i]+$q[3-2*($<6)-($i<2)],$t) + $v
                $k = $k + $t
              EndIf
            Next
    
            If 1=($k^)
              $o[$-4,$i] = $k
              $ = 7
              $i = 3
;            EndIf
;          EndIf
;        EndIf
;      Next
;    Next
;  Next
EndFunction
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