Cook and Chef are mostly same except Chef have degree and experience it can be rejected because of it but i don't think it had anything to do with Occupation you applied for.It can be because you didn't submit your Reference Letter for your occupation. Did you submitted your all Employment records,chefs degree,Bank statements/Balance Certificate,pay slips,tax returns,medicals?which of these documents you might have missed to submit.Maybe they might have ringed your past & current employers about your employment there. After getting ATIP you can surely re-apply again with more proof and documents and surely will get approved with your Skilled occupation.