Yes, it is common to prefer viewing the board in either 2d or 3d over the other option. There are people the opposite of you that see things much better with real pieces than they do on a computer screen. It comes down to how you do most of your work.
I found this in myself as well. I tried to combat it by doing chesstempo problems on a real problem for a couple of hours before an otb tournament. It seemed to help a lot. Since then, I try to do a large portion of my chess study/work on a real board. I even do my self-analysis with a real board and pieces plus a physical pencil and paper.
I have been playing here on chess.com and chessmagnet school for five years or more, and something has happened and I would love to hear any ones imput if I am hallucinating, or this is possible. I am not just, but much stronger analyzing the best move, on the flat screen looking at the pieces then three dimensional life like pieces.