I'm going to sound like a generic band instructor here, but practice your arpeggios. Start slowly, making sure your get down your tone on each note, and try to get them all to 1/8 notes or faster, without cracking notes. Also, check out http://www.laurenteachesflute.com/
, she has a few vidoes on embouchure. Even though you're doing well with high and low notes, you may be changing your lip positions too much to get to each octave, making it hard to focus on the middle octave. I know this because I had that struggle, once.