In those two years I've been practicing as well
I think that started when I changed my strings.
Clarify - is it sort of a vibrating sound? If it is, that on top of the fact you say it happened after you changed your strings and it happens on open notes leads me to think that you just need to put a few more windings on your A-string next time.
It's a problem pretty common to all Fenders - where there's not enough downward pressure on the nut from being so high up on the tuning peg, which causes the string to vibrate in the seat.