First of all: for the second MainWindow use grid instead of pack, so you don't need all those frames.
I wrote a small script, where you can see how I would do what you want (I hope it is what you want :-)):

use Tk;

my $top = new MainWindow();
my %density = (
                DI => "1",
                HF => "1.16",
                NH4OH => "0.9",
                H202 => "1.11",
                HCl => "1.18",
                H2SO4 => "1.84",
                Citric => "1",
                NH4F => "1.01",
                TMAH => "1",
                Nitric => "1.415",
                Acetic => "1.05",
                Phosphoric => "1.7",
                IPA  => "0.79"
            );

my $i = 0;
for my $x (keys %density) {
    $top->Radiobutton(
        -value=>$i,
        -command=>[\&colorme, $i])->grid(-row=>$i,-column=>0);
    $top->Label(-text=>$x)->grid(-row=>$i,-column=>1);
    $entry[$i] = $top->Entry(-bg=>'white')->grid(-row=>$i,-column=>2);
    $entry[$i]->insert('end',$density{$x});
    $i++;
}

MainLoop();


sub colorme {
    my $i = shift;
    map{$_->configure(-bg=>'white')}@entry;
    $entry[$i]->configure(-bg=>'black');
}
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