I spent a year studying nationalism and ethnic conflict, and I would say there is no consensus on this question (though no one I've read argues that it's exclusively ancient hatreds that causes these conflicts.) I would say that the term 'ancient hatreds' is generally used to describe the position an author wants to attack, rather than being actually held by any serious scholars today.

Donald Horowitz's book 'Ethnic Groups in Conflict' is one I've found useful, which trends more towards giving 'ancient hatreds' their due, though of course he emphasises how so much depends on how differences are mobilised by political actors.