It does make a difference. You must use A or B. Use B as it has become the default. You cannot simply match the colors to each side. They are twisted to prevent crosstalk. If you didnt use A or B, you must recrimp the ends.
Your assumption is perfectly logical, but not correct. It all started with telephone wiring. The primary telephone line was assigned to the center 2 pins of the RJ-11 connector, and a second line was assigned the outer 2 pins. This allowed a one line phone to work in a socket wired for 2 lines. (Yes, they could have kept the pairs adjacent, but they chose not to). When the 4-wire RJ-11 was expanded to the 8-wire RJ-45, the assignments for the center 4 pins were carried over from the RJ-11, and each of the two new pairs was assigned the adjacent new pins on either side of the original 4 pins.
That would be interesting to see the pictures if it's not too much hassle. The difference between "A" and "B" is that the green and orange pairs are swapped in their positions. The blue pair is always in the middle, and the brown pair is always on the end. As long as a cable is wired with a pair in the middle and on the two ends, and the last pair straddling the middle pair, it should work ok even though a nonstandard scheme would confuse the heck out of anybody looking at it.
RJ-45 punch down blocks and patch panels don't necessarily have colors labeled in the same order as the T-568A and T-568B standards. Most of these labels also have numbers for each position and if you look at the label in sequential order it should match T-568A and T-568B. Most punch down blocks give both color codes.
