should (@columns-3) maybe be ($columns-3)?

No, there is no variable named $columns. In scalar context, @columns is the same as scalar @columns, which returns the number of elements in the @columns array. Since you want 3 less than the total number of array elements, @columns - 3 is correct.

Can you take a look at the scripts and let me know where the problem is, as I can't understand it?

The problem is with these lines in the second script:

my $result = printf ...
...
my $data = printf ...
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In both cases, printf should be sprintf. The latter returns the formatted string, which is what you want; the former returns “true” on success, hence the 1 numbers in the second output file. As the code now stands in the second script, the line my $data = printf $output ("%10.3f",$c); prints the formatted output to the output file, and sets $data to 1; then at the end of the for loop, all those 1s are printed to the file. You need something like this (untested):

my $result = sprintf("%8.3f", $col3); # column 3 format

# loop over remaining columns
for my $c (@columns) {
    my $data = sprintf("%10.3f", $c);
    $result .= " $data";  # append $result
}

print $output "$result\n";
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Note that with this logic you don’t print to the output file until after the loop finishes.

Hope that helps,