What is a good program to check if your FLAC files are good and not transcoded 320 MP3s?

There's unfortunately no 'one stop shop' for it. There's a couple programs that can make guesses but they aren't very good at actually being accurate.

You can check individual files with Spek, Audacity, Adaobe Audition etc but you kinda need to know what to look for. Sometimes they are very obvious, sometimes they aren't...