Both strings need struck with the same amount of pick and force of the pick. It is real easy to strum the E string harder than the others. Watch your pick see how it hits the E string then bounces off it to the A string and bounces off of the A string while never hitting the A string like the E string.
Changing how you hold the pick will help your fingers feel how the pick is hitting the strings. This is one of those things that take hours to get good at.