I don't get head aches from it and it can't be blinking because it happens immediately.  I guess it could be distence.  It's almost like I zone out into the 3D... I could have a form of dyslexia.

Most definitely not alone with that one. While I can play in 3D for a decent while, I usually end up turning it off after an hour or so of use. Still, I haven't tried some of the techniques mentioned above yet. I was unaware that your eyes could actually acclimate to the strain over time...

I don't often watch 3D movies but when I never get this experience, however, I have not tried high end 3D.

I felt the same way until I bought a 3DS. First of all, you need to find the distance and position you're comfortable at looking at the screen. That's hard to do on a store display.

Second, 3D just isn't good for everything. I primarily play the 3DS with 3D off, it can be distracting. However I always turn it on while playing Mario Kart.

My advice, ignore the 3D aspect if it doesn't appeal to you. Most importantly the 3DS has great software and has already become my favorite handheld system.

I hardly use the 3D on mine. It never really impressed me and I would rather save battery life.

That is the problem. You're not supposed to crank it up to the maximum. You're supposed to adjust it to the point where you can see the 3D but it doesnt strain your eyes.

I dont have it on all the time cause i want the battery to long last aswell, but i have no problems with it, aside a second of readjusting to reality after playing.

you get use to it (ie. trian your eyes)

Same thing use to happen for me with 3D movies. Now all dandy.

You get used to it. I don't feel anything anymore.

The 3D took some adjusting to for me, but once I was used to it, the problem permanently went away. I almost always play with the 3D on full-blast now.

yup 3d sucks join the i hate 3d club with me :D