The button is a known issues, some plugins like Shortcodes Ultimate decided to not add their button to the TinyMCE editor (like they should) and add a button above for some reason. I guess it’s more visible.
Unfortunately, it’s not the right way to do things when it comes to the editor, and it breaks functionality when other themes or plugins make use of the editor like we’re seeing with Sections.
Since it’s such a popular plugin, I’m working on integrating it – although I wish they would just stick to WP coding standards.
As for stripping the shortcodes – that shouldn’t happen. Is it a specific shortcode this is happening to?