That's a strange one. I'm wondering if the shortcodes are being triggered at all (or maybe too soon). Could you try delaying it by by editing toc.php and on line 129 change from
add_filter( 'the_content', array(&$this, 'the_content'), 11 );
add_filter( 'the_content', array(&$this, 'the_content'), 100 );
I currently have this in trunk and have it ready to be rolled out in the next release. This simple change makes it more friendly with SEO related plugins that try to munge anchor links on the current page. Hopefully it works for you too.
On discussion of the TOC appearing on landing pages when set to automatically trigger, I have tried to limit it to appear appropriately on the correct page but may have missed some. The exclusions I currently have are:
!is_search() && !is_archive() && !is_front_page()
How is your landing page created? Was it hand crafted? If so, try using the_excerpt rather than the_content?
Did you experiment with the TOC+ widget by any chance? If so, make sure you disable the "Show the table of contents only in the sidebar" in the widget, then save, then remove the widget.
Finally re failed saving. I would firstly suggest to verify that the message actually originates from TOC+ as I've come across many themes and plugins with a global admin presence to this same effect (eg they have a global form/notification area in the admin section which can sometimes get in the way). Secondly, once verified that it comes from TOC+, it results in this only if your nonce security tokens do not match (eg your sessions differ; you didn't actually request a change; you submitted from an unknown link). When you visit the settings page, it does NOT initiate a save operation until you click the update options button. Check out nonces for more information.