Midwest Airlines Midwest Miles (Pre-Alignment) - Which "airline" would I actually be flying

Looking at a trip from BOS to MSN in December; some of the BOS/MKE flights say they're operated by Frontier; Frontier doesn't currently fly to Boston and when you check their site say that their BOS flights are handled by AirTran...however the flights don't match up to anything offered by AirTran.

Is this just an instance where the Frontier and/or AirTran websites haven't caught up yet?

You will be on a Frontier plane flying for Midwest under the new codeshare.