something which should help your thumb, is to do your best to play it SOFTER and more quiet than the other fingers. This will "balance" your hand better.
The essential thing is to play slowly. Play in a tempo where you feel that you have total control, and no notes become extra marked. When it works, increase the tempo but just a little bit.
You'll probably notice that playing different tonalities will produce different extra marked notes. Listen carefully, and find out why these notes are extra marked. Is it because of the finger hitting the note? Is it because it's a black key? If you are aware of WHY it doesn't sound good, you have better chances to improve your playing.