I successfully created my own shortcode to display in Simple Pages. It works when the shortcode just displays simple text, and lets me put PHP/HTML in the shortcode, but when I go to view the page/page source, all of the PHP tags are commented out. This also happens for some basic Omeka shortcodes. I have HTML filtering turned off in the Security settings.
Possibly related issue: on my Plugins page, there’s no “Configure” button for Simple Pages.
Can you clarify what’s happening, particularly the part about it also happening for some of the basic shortcodes? I’m not quite sure what you’re putting in the page and what’s getting stripped or commented out.
It coming out inside comments is a little odd, I’m not sure what’s happening there.
At any rate, you can’t usefully output PHP code in a shortcode anyway. Your code needs to execute inside the shortcode function and return whatever output it’s supposed to directly.