I had this same issue to some extent for a while. I didn't have anyone to play with in-person and I had trouble adjusting from 2d to 3d. My advice is simply try to find more opportunities to play over a real board. Once I found a bi-weekly opponent I found my real-life games getting stronger and pretty much matching with my online strength.
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I seem to have the opposite problem. Stuff I can do on a real board I can't do on 2D.
I'm just like Immanuel .. I have the opposite problem that you have
I played chess on real life for something like 2 years and I found me in a very difficult position when I want to play in my computer .. I guess it just gets better with lots of practice, so play as many times as you can and you will go over that problem (:
I have a strange problem. I play a lot of internet chess and once in a while I get to play face to face against few of my friends on a real chessboard. Now these guys are really smart people but they are not chess geniuses, I often beat stronger opponents on chess.com. But because I am used to play on 2D board with 2D pieces I get incredibly confused when faced a real 3D board and pieces. It's like my brain completely shuts down not being able to find even the most simple combinations that I usually find easily. As the game progresses, the board starts to look like a vast forest of pieces that I just can't see clearly and handle it properly so I find myself in troubles soon after the opening . For over a year now I haven't beaten a face to face opponent and it's starting to worry me a lot. If anyone has similar problems and cares to discuss them please post it down.