You do realize there are 2 kinds of TOC?
The Calibre-Viewer (really is EPUB) uses the NCX
The Inline (HTML) TOC is just another text file with a Semantic Flag
If you are using Headers (H1-6) to markup, They belong IN the Chapters, not the Inline TOC (If you want them to actually be useful

)
If you want to Manually mark/unmark, use the TOC tool, available in the Main UI or the Editor.

Read about various Formats in the MR Wiki (link at the top of every page)