My first question is whether or not you have a teacher? Actually watching you with an expert eye would go a long way.
My only advice is to practice slow. Start with whatever tempo allows you to play the scale evenly, and slowly build up. Concentrate on technique, lifting the fingers and to go deeply into the key. Mix the tempo up on your scales - for example play dotted quarter/eighth note rhythm, and four fast/four slow etc.. Make sure your hand is relaxed, one sign for me that I am tensing up is my pinky wants to fly out. Make sure when you play the scale this isn't happening. If it is, slow down again.
Don't be afraid to go slow, for as long as it takes.
Without seeing what is going on it's tough to really say what to work on, but passing the thumb under smoothly is a skill that needs to be mastered. It needs to be learned. You can "jump" - playing thumb over, but imo you should master thumb under.