Oh, I've done the calibration. I thought it was just a 'stepper motor calibration' and not a 'steps per mm' calibration; didn't realize they were the same. I'll check them again to make sure they're still correct.
I don't move the gantry by hand at all when power is on, but I do when it's off, is that ok? Prior to powering up, I pull my gantry forward and use precision blocks to align the Y plates and then turn on my machine. It should always be square when I power it up by using this method.