People are getting worked up over comparing the before and after wave forms way too much. The point of mp3 encoding is not to preserve the wave form, it is to throw away as much as possible without affecting the perceived sound quality. Unless the wave forms are exactly identical, the pretty picture tells you nothing.
(Well, ok, if you see important frequencies getting chopped right off that's bad.)
If you want a high quality compressed sound file, you don't use mp3.
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