Alternate Picking/speed Picking

Hello everyone, something is really bothering me today.After so much practice in alternate picking, with lessons such as Neoclassical Etudes #1 & #2, String skipping Etudes, Modal Madness Series, I came to the conclusion that I might be doing it all wrong.
I have been playing guitar for quite a while, so I can reach a decent speed with alternate picking for a intermediate player.

As I play in slower tempos, I find no problem in the way I pick. Up and Down , pick angled, all that stuff. The notes come out clear, no problem , I'm happy.

However,when I start to add some bpm to the tempo, in order to be able to play faster, I notice that my picking hand starts to do some kind of a diving motion, and very often the pick hits the pickups (The distance between the strings and the pickups on my Ibanez is not very big).

I can still make the notes sound, but I feel like doing this motion kind of stops me from going on to higher tempos.The pick doesn't just lightly scrapes the string, it goes deeper and hits the pickups.

I'm not sure I've made myself perfectly clear, but does any of you guys experience the same problem? If so, how did you fix it?

Thanks in advance.

Video : https://www.youtube.com/watch?v=t7nKMdRmARs...eature=youtu.be