The curse of the Arduino offset header! You will encounter the same thing on the boards with the Uno style form factor too (Leonardo, Due, Zero). Luckily there are some sane boards like the Nano, Pro Mini, Pro Micro, MKR boards, etc.
sylvain_van_iniitu:
any workaround to this problem ?
One possible solution is to simply not use the pins on the offset header. You have so many pins on the Mega so there's a good chance you don't need those. That's more difficult with the Uno-style boards since they have less pins.
There's some trick with bending the male header pins so that the will offset the screwyness. Someone was selling those for a while but I don't remember who it was.
sylvain_van_iniitu:
I think that's a good solution.
sylvain_van_iniitu:
and also, is there any good reason to this strange spacing ?
Arduino made a newb screwup many years ago and instead of just eating the loss and fixing their mistake, as any responsible business would have done, they unleashed this curse on the entire world and now that idiotic offset header format has leached its way into so many products. See:
http://forum.arduino.cc/index.php?topic=22737.msg171839#msg171839