I find the same thing. Crappies tending to be higher than blue gills. During ice fishing, we run a lot of double rigs, our bottom rigs will mostly be setup for blue gills fishing close to the bottom. When we see a mark come in higher in the column, we come up and fish them with the other jigs. We run two different baits. One that appeals to gills, one that appeals to crappies.
One thing to consider here. Bluegills predominately feed on plankton and zooplankton wheres crappies will feed on your bigger lavea, insects, and minnows. As the sun begins to come up, plankton and zooplankton go towards the bottom in order to get away from the sun. The blue gills will follow the plankton and zooplankton. If you ice fish and have a flasher, you will know what I am talking about. As the day progressess, these fish will go deeper and deeper until they are on the bottom. As the sun starts to set, the plankton and zooplankton rise towards the top bringing the bluegills up with it. Because if this, later in the day, when the sun is going down, this is when we find the vast majority of crappies and bluegills mixed together. For the most part, the crappies are staying somewhere in the water column. When that plankton and zooplankton meet that desired depth, the gills also meet that desired depth.
Just food for thought but, on average, this would be the reason why your crappies will be higher in the water column during the day, and "might" be lower in the column right before dark.