I've never heard of a Magister degree, just a Master's degree. But looking it up on Google, it tells me it's a type of Polish school degree, and is the academic equivalent to a Bachelor's degree. But I'm not sure at all.
They mean actually the same thing. Magister is the Latin word for Master. Several Universities around the world prefer to use Latin terminology, also in some professions Latin terminology is used indistinctively, i.e. doctors and lawyers.
magister -tri m. [master , chief, head, director];