Just a minor nit-pick -- the day-of-week stuff could be handled a little more easily:

...
#Create Labels and headings
my @wkdays = qw/M T W R F Sa Su/;
my %labelColumns;

my $i = 0;
foreach ( qw/On Program Browse/, @wkdays ) {
    $labelColumns{$_} = $i++;
    $mid_frame -> Label( -text => "$_", -relief => "sunken", -padx => 
+5 ) 
        -> grid( -column => $labelColumns{$_}, -row => 0, -padx => 0 )
+;
}
...
    # Time Checkbuttons
    for my $dy ( @wkdays ) {
        $mid_frame -> Checkbutton( -variable => \$files[$index][$label
+Columns{$dy}])
            ->grid( -row=>$_, -column=>$labelColumns{$dy}, -padx => 0,
+ -pady => 5 );
    }
...
[download]

If/when you decide to change an option or something for those mid_frame Checkbuttons, you'll appreciate having only one line of code to change, instead of 7.