Probably normal. At the end of winter, there was next to nothing in the boxes other than bees and the clustered at the top, having eaten most of the stores. They will start brood production where they are clustered, and so they started up in the top box. I'd guess all the brood up there is capped and or emerging, and there are some drones, right?
Once the weather warms up, they will move down, especially once there are large numbers of bees in the hive, this is normal behavior. Unusual to skip a box, but if it was full of early pollen, also common, they moved the queen down to empty comb to raise more bees, and will work back up to the middle box shortly, it they aren't already up there.
My bees this year started brood up in the honey supers I foolishly left on, but by last weekend all that was left up there was a scattering of capped emerging brood and capped drone cells. They were back down in the deep with lots of capped brood (now emerging, the cappings are on the sticky board under the screen) and they are using the mediums on either side. More or less pollen bound at the moment, but that will fix itself shortly as they aren't bringing in as much at the moment, just lots of nectar. They will start on pollen again in a few days as the brood emerges and the queen lays more eggs.
I will be checking to make sure they don't back fill and swarm -- I need to pull a frame of brood for my package anyway, so I'll tuck in an empty frame of drawn comb, should avert swarming behavior. No signs of queen cells last week either.