multiscreen HTML 5 output in Chrome – when scrolling down very long topics in the content pane the navigation area 'moves up' , i.e cant see search field or TOC.

This is by design. If you want to change this, the content section must have a set height and scroll. Which layout are you using? -- Check out the Responsive layouts and the Social layout. I believe those have the more traditional TOC placement.

Kind regards,

Willam