You made $File1 an array.
You should do something like Mart said
Code:
For Each $F in $File1
	;Do stuff
Next

Here is a modified script. Do not forget to add the DirList() UDF at the end.
If NOT @LOGONMODE
    Break On
Else
    Break Off
EndIf
DIM $RC
$RC = SetOption("Explicit","On")
$RC = SetOption("NoVarsInStrings","On")
$RC = SetOption("NoMacrosInStrings","On")
$RC = SetOption("WrapAtEOL","On")

DIM $objExcel, $Files, $FilesDir, $File, $File2, $Value, $Values[1,0], $i, $j
$FilesDir = "D:\scripts\test\xls\"
$File2 = "D:\scripts\test\Workbook2.xls"

$objExcel = CreateObject("Excel.Application")
If @ERROR
    ? "Error creating Excel object"
    ? "Error " + @ERROR + ": " + @SERROR
    Quit @ERROR
EndIf

$Files = DirList($FilesDir,2)
For Each $File In $Files
   
    $i = -1
    ReDIM $Values[1,0]
   
    $RC = $objExcel.Workbooks.Open($File)
    $Value = $objExcel.Range("C6").Value
    $objExcel.Application.Quit
   
    $RC = $objExcel.Workbooks.Open($File2)
    While NOT $objExcel.Range("A"+($i+2)).Value = ""
        $i = $i + 1
        ReDIM preserve $Values[1,$i]
        $Values[0,$i] = $objExcel.Range("A"+($i+1)).Value
        $Values[1,$i] = $objExcel.Range("B"+($i+1)).Value
    Loop
    $objExcel.Application.Quit
   
    For $j = 0 To $i Step 1
        If $Values[0,$j] = $Value
            Move $File $Values[1,$j]
            If @ERROR
                ? "Error moving file " + $File
                ? "Error " + @ERROR + ": " + @SERROR
            EndIf
            $j = $i
        EndIf
    Next

Next