Lose all the foam, the case, and the e609. Put the 57 about 1/2 inch away from the centre of the speaker, and about 1/2 inch off the grill and try again. I have a shitty room and I never have phase/reflection problems, so I don't think you will either. Just simplify things because you obviously still have a problem.
Ok, back to the open air...
As you said, 1/2 inch off, 1/2 inch away...
http://dl.dropbox.com/u/3106634/BoHM_57HalfInch_M.mp3