but I'm missing something obvious

Yup, you are missing a stand alone sample that demonstrates the problem. At the very least a little sample data would help. It doesn't help that the code you do show demonstrates neither the frame related issue nor the non-frame related issue - it's somewhere between the two!

However, reading somewhat between the lines, the following may get you to where you want to be:

#!/usr/bin/perl
use strict;
use warnings;
use Tk;

my $mpy0    = 0;
my $mpe0    = 10;
my @data_in = <DATA>;
my ($model, $initial, $copyerr, $LST, $file_id, $tm, $format,) = split
+ /[|]/xsm,
    $data_in[0];
my $for2;

if ($format == 1) {
    $for2 = q{comma delimited};
} elsif ($format == 2) {
    $for2 = q{tab delimited};
}

my $mw = MainWindow->new ();
$mw->geometry ('500x600');

my $lab0 = $mw->Label (-text => "Model $model")->pack                 
+();
my $lab1 = $mw->Label (-text => "Initial #: $initial")->pack          
+();
my $lab2 = $mw->Label (-text => "Copying Error % +/- $copyerr")->pack 
+();
my $lab3 = $mw->Label (-text => "File Format - $for2")->pack          
+();

#Geometry Management
my $table = $mw->Frame ();
my $lab4 = $mw->Label (-text => "Year");
my $mpy_0 = $mw->Entry (-width => 5, -textvariable => \$mpy0);
my $lab5 = $mw->Label (-text => "Momentary\nPop. Est.");
my $mpe_0 = $mw->Entry (-width => 5, -textvariable => \$mpe0);

$lab4->grid  (-row => 1, -column => 1, -in => $table);
$lab5->grid  (-row => 1, -column => 2, -in => $table);
$mpy_0->grid (-row => 2, -column => 1, -in => $table);
$mpe_0->grid (-row => 2, -column => 2, -in => $table);

$table->pack ();

my $button = $mw->Button (
    -text    => "Submit",
    -command => \&somesub
)->pack (-side => 'bottom');

MainLoop;

print qq{$model|$initial|$copyerr|$LST|$file_id|$format|$tm|$mpy0,|$mp
+e0,|};
exit;


sub somesub {
    $, = "\n";
    print "\nWorking\n";
    $mw->destroy;
}

__DATA__
1|0|0|0|0|0|1
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