I thought I was crazy for thinking this too, but I have noticed that it takes me a couple of games in OTB to get used to the board setup after playing a lot of online chess. It's almost like the different perspective changes the gameplay.
Is 2D hurting our OTB ability?

Yes, it's different but I wouldn't say it HURTS your OTB chess. As long as you still play OTB once in a while you'll still be fine. Studying tactics online with 2D won't help your OTB play as much as if you studied them on a 3D board, but of course it's alot faster and more convenient and you can do alot more-- so in the end it is better [consider doing 100 problems on the computer at 75% benefit each, or doing 25 on a board at 100% benefit each (because of set-up time)]. Plus it's not just that you get used to 2D, I think 2D is easier to see in general :)

I think it helps and hurts. Like all above have mentioned, that you can see all of the pieces and a lot easier. But I noticed that when i studied my games on Chessbase with an engine running that regardless of whether or not it is 3-d i am still learning. I think it will help in the sense of you are playing and comprehending. When you play OTB i think it has a lot more to do with the Pyscological aspect. How comfortable the chair is, who your opponent is, their gestures, their smell, everything. BUT when you are at home, you are in your comfort zone, so you dont care about these things. So i would say that perhaps it is just the fact that you are flustered by these things.
I also find when i play online 2-D chess all week then on Sundays when i play at mac donalds it will take a few 5 min blitz games to feel normal.One thing i started doing is every sunday morning i load up chess master 11000 an play a few blitz games against the 3-D board which i find to be about the best 3-d board for a computer.I think if you do this it may help.When i went on the web i noticed Aol had a chess on line play headline i played two games gave up a draw in first game my 2nd game i was used to the 3 d board an won easy.I recomend cm 11000 only for the 3-d board which is a very good for a computer monitor.

You have got a point there! chess.com provides 3D pieces (premium players only) - but the perspective is so bad that I found it difficult to play with them.
I think we should practice both online and OTB...

I'm a little suspicious of this problem as well. When I practice analysis a la Kotov, play against the computer, or play through annotated games, I set up a board and work it out that way. But it's too inconvenient for me to set up a new position for every single tactical problem I do when I can just whiz through them using a computer.
When we play online we are playing in 2D (2 dimensional=flat pieces)
We also see over the board instead of at an angle like when you sit at the table and play.
When we play over the board in real tournaments it is in 3D.
So is online play/study useless? Or does it not matter?
I've noticed I can solve tactics online a lot easier than I can solve them over the board.
And online I see the whole board and all the pieces, but in real over the board games I sometimes lose sight of pieces...
Am I crazy or am I right?
Should I study with a set and pieces or does it not matter?
Keep in mind I play in real tournaments and improving is my main goal.
Online chess comes second to USCF chess.
Anybody have any thoughts on this?
I think it hurts OTB. The other day I thought maybe I would play an online game, but set up teh pieces on my chessboard at home. I couldn't see combinations on the physical board that I easily picked up online.

I think this is a silly notion. Chess exists in the mind; the board is just a point of reference. It matters nothing if the board is 2D, 3D, or nonexistent. When I'm visualizing OTB, the pieces are a distraction anyway.
Speaking for my self do find it hurts some however the overall practice helps.I think that if you load your best 3-D board.Fritz Chessmaster 11000 all hve good boards then play a few blitz games it will get you in to the live 3-D style of play.Most of the on line play web sites 3-D board are so bad it hurts to play on them.However a few programs such as listed above have good feel an look which will help you transfer back to playing live in person chess,Now when online servers start in time to haver good 3 -D boards to pick from this will help end this problem an it is a real problem for a lot of players.
definitely doesn't. In fact, I'm a better player because of live chess, OTB as well. I do know what you mean, though- seems strange at first, but halfway through a game it becomes fine.

I've had problems with OTB sight after playing a lot on here, but I've changed to the pseudo-3D pieces and that seems to have helped.

good question......usually when i play online and then go to the boards set up in my den to study positions,i become annoyed and distracted by the voices inside my head....but here's the weird thing, the voices that seem to originate outside my head don't really bother me....going from 2D to 3D does seem to trigger the voices...thanks for raising this question.....Just thinking outloud here................

If you do not play OTB once in a while, I think it can hurt your game play a bit. However, because I do far more analysis on 2D online games, it improves my logic more than it hurts it. Play OTB once in a while and you will be fine.

Chess as a logic game is fully represented in 2D albeit the "visuo-spatial ability" makes some more claims in a OTB game (i.e you can see topalov adjusting his pieces here at min 0:40 and kasparov at min 1:40, even though it can be a "flattery ritual" too it's quite usual).
Anyway, making practice in 2D in no way can harm you, it helps the very core skills of chess in my opinion. I agree with Estragon, pieces are just placeholders for your mind.
The "3D" chess sets here keep the 2D checkboard and so the pieces occupy a portion of another "2D" square, and this mixture of 2D and 3D may appear strange
When we play online we are playing in 2D (2 dimensional=flat pieces)
We also see over the board instead of at an angle like when you sit at the table and play.
When we play over the board in real tournaments it is in 3D.
So is online play/study useless? Or does it not matter?
I've noticed I can solve tactics online a lot easier than I can solve them over the board.
And online I see the whole board and all the pieces, but in real over the board games I sometimes lose sight of pieces...
Am I crazy or am I right?
Should I study with a set and pieces or does it not matter?
Keep in mind I play in real tournaments and improving is my main goal.
Online chess comes second to USCF chess.
Anybody have any thoughts on this?