Excuse me, sir, but I said nothing of a theme.
The checkbox to allow or disallow comments and its companion trackbacks has nothing to do with any theme. Both are native to WordPress.
Those pages where the checkboxes have been cleared (not ON) show the "unenhanced" comment form which allows a comment to be entered, which is assumedly then rejected by WP because the checkbox enabling comments is not checked.
Previous to the installation of your plugin, the WP settings were being handled appropriately by the theme. BTW, that theme is Weaver II Pro.
However, the behavior I cite is reproducable in Twenty-Thirteen as well.
I have marked this topic as "not resolved."