Some good and interesting ideas above. Suggest you work through Jbtsax's post first as he covers the most likely causes. If it's a problem with the sax (and these are very common, even on new instruments) it needs to go to a repairer. If it's new, the seller. Often helps if an experienced player can test the sax for you. And this could well be the seller - get them to demonstrate that it plays cleanly over the full range.
But we need more info - we're, so far, assuming that the sax is only playing in the upper register. i.e whether you play a note with the octave key or not, it's the same pitch, and this is the same over the range low D to C played with laft hand middle finger only. Please confirm this.
Most tuners will tell you which note you're playing, but not which octave the note is in. And unless you have a tuner with a setting for Eb instruments, you'll need to remember that when you play a written C on the alto, the tuner will show Eb if you're playing in tune.
Don't worry too much about the quality of the sound at the moment, just concentrate on getting the notes coming out at the right pitch. Once you've got this, you can start working on tone as well.
