Mail is not present in the my Kontact configuaration menu. My main toolbar in Kontact shows the mail icon (amongst summary, calendar etc) though when clicked it opens kmail in a seperate window, not within Kontact as previously.

Any help greatly appreciated.

Kontact will detect when the component apps are open separately and not include them in the all-in-one display.
You have to quit Kmail (using File -> Quit) first and then when you click on the Mail icon in Kontact it will open within Kontact.