New firmware question

I finally updated my firmware (Arduino Mega board w/ Ramps) and discovered (the hard way) that it changed my Y axis direction. It also seems that the steppers are a little more noisy than before during moves. I am still running the X and Y in parallel (vs series). I am also seeing the LCD flashing question marks where the X, Y, Z indicators are. It flashes between the X, Y, and Z and a question mark.

Are there any items I need to look at and change?

Nope that should all be normal.