With power off and the motors disconnected you can check the pairs of wires that show a resistance. It doesn't matter which you call A and B but when you connect them back up again, if the stepper runs in the wrong direction you just reverse one phase.

Having said that, I have found that a stepper plays up in the way you describe, it is a poor connection or broken wire. The Y axis on my 3D printer is the only one where a motor travels and I have replaced the cable twice so far because one conductor has fractured within the insulation. The symptom is when the print starts to lean to the right or suddenly has a big step in it, as the stepper movement seems biased in one direction. I have had the same with my CNC Z axis, which only wanted to go up. Again, the axis where the cabling does the most movement.

Bt you say it is happening on every axis - Hmmmm? unlikely to be 3 sets of bad connections or broken cables, but I would check it out.