I was able to see the resizing problem you described (using darwin, Perl 5.8.8, Tk 804.028). It stopped It became (or remained?) unpredictable when I changed the values assigned to the -command parameters in the widget creations.

Instead of this (whitespace adjusted for legibility):

    my $DoButton = 
        $mode_buttons->Button(
            -text => 'Continue',
            -command => sub {&do_setup()}
            )->pack (-side => 'left', -expand => 1);
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Try it like this:

    my $DoButton =
        $mode_buttons->Button(
            -text => 'Continue',
            -command => \&do_setup   ### provide a code_ref, not anon_
+sub
          )->pack (-side => 'left', -expand => 1);
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Also, wherever you had this:

     ... -command => sub {&getTool();&CleanUp();},
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I would replace it with:

     ... -command => sub {getTool();CleanUp();},   ### drop the "&"
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just on general principles.

I'm not sure I can explain why the difference seems to matter, but I should have known that such a change would just be cosmetic -- no reason it should affect behavior -- but still, wherever a -command parameter is simply supposed to invoke a sub with no args, the value of that parameter should be the code_ref that points to that sub.

And whenever you need to pass args to the subroutine, provide an anon.array containing the code ref and the args:

    ... -command => [ \&func_name, $arg1, $arg2 ],
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UPDATE: NEVERMIND! This is stranger than I thought -- the behavior I'm getting is not actually following a pattern yet. I'm seeing alternations between "resizes as intended" and "shrinks to unusable size". Perhaps someone else will figure it out while I'm struggling with this...