As I have recently gotten a new PC at work, I have not yet installed all of the various tools I use, so I don't have Tk handy to try your code. However...

In your check_sub subroutine, at the time of this reply, all of your checks will be listed. Are the values of $check1 though $check16 what you expected?

I did notice that you have:

-offvalue => 'NOT CHECKED')->pack(),
-command => print OUTFILE "$job8\n";
[download]

It should be:

-offvalue => 'NOT CHECKED',
-command => print OUTFILE "$job8\n")->pack();
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Also, you could use arrays in your code. Something like (not tested):

my @jobs = qw( 18L 07O and so on );
my @checks = ('NOT CHECKED') x @jobs;
my @buttons;
my $i = 0;
for (@jobs)
{
    my $buttons[$i] = $check_frame->Checkbutton
    (
        -text => $_,
        -variable => \$checks[$i],
        -onvalue => '    ADDED',
        -offvalue => 'NOT CHECKED',
        -command => print OUTFILE "$jobs[$i]\n"
    )->pack();
    $i++;
}
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