G'day roho,

To get the pairs of checkboxes aligned with the left border, you'll need to add -fill => 'x', e.g.

$frame_cb0->pack(-side => "bottom", -pady => 1, -fill => 'x');
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However, that only aligns the first checkbox in each pair; the second checkboxes will have dog's hind leg alignment:

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To align all boxes in a tabular fashion, I'd use Tk::grid instead of Tk::pack.

[Hint: to see what parts of the overall window are covered by particular widgets, give them a background colour which stands out, e.g. Frame(-bg => 'red', ...), Checkbutton(-bg => 'blue', ...), etc.]