say "$lnPAM1[$i][$j]:$i:$j";
[download]

When I do this I see something like this snippet:

-3.91202300542815:3:7
-3.50655789731998:3:8
:3:9
:3:10
:3:11
:3:12
:3:13
:3:14
:3:15
:3:16
:3:17
:3:18
:3:19
-4.60517018598809:4:0
:4:1
:4:2
:4:3
[download]

Taking a look at where the matrix is built, it seems that the problem stems from your use of next in:

LINE: for (my $i=0; $i<20; $i++){
    for (my $j=0; $j<20; $j++){
        if ($matrix[$i][$j] > 0){
            $lnPAM1[$i][$j] = log $matrix[$i][$j];
        }else{ next LINE;
        }
    }
}
[download]

By using next, you don't use all 20 iterations of i or j when building the matrix, but you do later on. You could look to see the dimensions of the matrix before iterating through its dimensions.