Probably the truss rod is adjusted at the heel, as has been said above, remove the PG and check.
I think there has to be be a sticky about set up, check it out.
Anyway, if you have fret buzz on higher frets, your saddle is still adjusted too low.
A too tight truss rod will produce fret buzz on the lower frets.
If saddle height adjustment becomes 'abnormal', you should consider shimming under the neck heel to change the neck angle (piece of cardboard or credit card).
...it's a shame that they're teaching all these note scales as a way of learning jazz, and that's not the way to do it...