Now, I don't know how you are practicing your scales. If you are playing only the first note and then pulling off or hammering on the remaining ones then it might be that your difficulty is down to finding pull offs harder than hammer ons. This is quite natural. I suggest you practice hard at pulling off.
If you are picking every note then I don't know why you might be having this problem unless it's cause you fall into the common trap of spending more time practicing going up than down; that buildup of drama that comes with increasing pitches can unbalance one's technique you see.
Anyway, try this exercise, it might help. It's supposed to be hard, I know it's dull but you could always jumble the notes up to make it more exciting. It'll be bound to increase your finger strenght if you keep practicing but don't strain yourself; tendonitis finishes some guitar player's careers.

http://www.guitartricks.com/2000/trick.php?trick_id=6032