Most of the information I've seen thus far are treat these acronyms as being synonymous with each other. I've heard however that MFR should be used with polypropylene while MI should be used when talking about polyethylene.
If you're interested in the more technical side you'll find that the MFR of a material is an indirect measure of a materials molecular weight. Thinking of spaghetti is often helpful. A bowl of long noodles will 'pour' a lot slower than a bowl of short noodles.