Your submit handler overrides other custom submit handlers

When you set your submit handler you do:

$form['buttons']['submit']['#submit'] = array('publish_submit');

And then call the regular node submission in your submit.

This means that any other modules that have added their own custom submit handler have it overwritten and it never runs, which is obviously not good.

This module should add its submit to the others instead of replacing. Like:

$form['buttons']['submit']['#submit'][] = 'publish_submit';

or

array_unshift($form['buttons']['submit']['#submit'], 'publish_submit');

or something.