I know that you mentioned that it wasn't the brakes, so I would tend to think it is the wheels. It could be that the bearings need to be repacked, or perhaps the adjustment it too tight on the bearings and the wheel can't roll freely. It might be something that new bearings/grease will help.
The one thing that I always remind people of is to compare only that set of wheels, quite often we compare it them to more expensive wheels which better quality bearings, races, seals etc...
Let us know what you find out!