Same recipe but sometimes white chocolate cookies come out strange I always use the same recipe (weight everything including eggs) but occasionally the white chocolate cookies come out funny.

When baking in the oven I can see them making bubbles constantly, they always come out flatter and taste doughy.

Here is a video showing the bubbles while in the oven: http://youtu.be/ZLA1h3HzkXY

What could be happening here?

Note: I melt the butter, use a bit of baking soda and bake them from frozen. But it only happens with white chocolate, that's what is strange!

From the same dough batch that was divided into two:
White chocolate has a higher fat content than milk chocolate.  That's very likely throwing off the balance in your dough.  Even though you're using the same batch, more fat is being added to the white chocolate cookies as the chips break down.

You may need to reduce the butter or margarine that you use for the white chocolate cookie dough by a bit.  It's probably a very fine difference, perhaps 10-25% less butter.  That's a bit of a guess but please let us know your results if you give this a try.