Panos, first of all, welcome to SimHQ!
Second, from the sound of it, this is your first time flying the Falcon, yes? Have you played Allied Force or Falcon 4 or other "flavors" of Falcon before? If not, be aware that BMS is not exactly newbie friendly --- but don't let that put you off --- this simply means that the sim requires more study than usual and the docs are not written in a newbie-friendly way.
Your best bet is to join a virtual squadron who can teach you the ropes or at least fly with someone who knows what he is doing. I would advise posting on the BMS official forums, but it's chaotic over there and a new guy can be lost easy.... ask one question, get 15 different answers from 5 people.
Good luck, and if you have any specific questions, do post them here and we'll see how we can help.
Re: key assignments, might be there are two or more keys assigned to different commands? Or exit the game, enter again, and see if this behavior shows again. I've had that happen to me a few times, confused me too, but not happened again.