There is no difference in meaning among それぞれ, それぞれに and それぞれが in the fist example.
As for the second one, the meanings are ambiguous for all of それぞれ, それぞれに and それぞれが. It can mean "Each of them spoke all those three languages." Furthermore, especially when the subject is two persons (e.g. トムと太郎はそれぞれに英語、日本語を話した), それぞれに can mean "to each other (Tom talked to Tarō in English, and Tarō talked to Tom in Japanese)" since に indicates the target of 話す. You need to say トムは英語を、太郎は日本語を、フィリップはフランス語をそれぞれ話した to avoid ambiguity.