I've read more than one legitimate literature reference implying that you should stare at your real board, then input the moves into the computer. Certainly, if you WILL be playing OTB chess, this is a wise practice. Indeed, most psychological studies corroborate practicing under the same conditions that you wish to perform in (e.g., listen to the same music while testing that you use while studying). However, only LONG games are truly practical in this regard as you will surely lose on time trying to play on two surfaces at the same time, though perhaps the first 20 moves of long BLITZ might be accomplished in this manner.
Short answer: Yes, I see it. And probably to some degree, we ALL see the effect.
I'm not good at playing chess in the computer, when I play a game here I set the pieces in a real board, see the position, make a decision and then go back and make the move in the computer.
I've tried online blitz chess and I hang pieces all the time, even though I'm not a beginner and I'm not a bad player, I blame it on ergonomics since this doesn't happen when I play "live" chess with a chessboard.
I really think that ergonomics (or HCI) have a lot to do with it, somehow I can't see chess well in 2D.
Do any of you experience the same?