I'd say it would depend on the tone and body language in which it was said; the words themselves, "where have you been?", could easily take on multiple meaning depending on inflection and delivery.

It could be small talk, and maybe it might be a cultural difference, but the words alone (without taking inflection, etc into account) sound accusatory to me; if they were really wanting to know where their coworker had gone to lunch, and whether it was any good or whatnot, I would think they would phrase it closer to what you wrote, rather than what the OP has stated.