Hi Sarah,

When you're muting in a comfortable position, look at your strumming hand where it's resting on the bridge and you'll see that it's kinda at an angle from right down to left so the low E string is the first one to go unmuted, that's what makes it louder than the others. You can either re-position your hand so it's more in line with the bridge (straight up and down) which feels a little unnatural..or
Try moving your (strumming) hand slightly left or right while you're playing muted power chords to see what sounds better. I would experiment by sliding my hand back till it wasn't muting the strings anymore..then slowly moving it onto the strings until I got a sound I liked.

I hope this isn't too confusing, it's so much easier just to show someone!

Neal
GT Channel Host