I think I found a bug in atahualpa 3.4.9 (and maybe in never versions too)

Go to:
Posts & Pages -> Edit POST/PAGE INFO ITEMS -> KICKER: Homepage

When I put %category-linked% into it, right sidebars disappear from homepage.

I don't get the symptom in 3.5.1

Jazoj, it's possible that you made a coding error and it caused WordPress/Atahualpa to throw an error and not completely generate the page. To check that I need some more info, like the version of WP and what is the url?