Is the monitor mounted upside down, and the SF board had it's output flipped?
I checked the service manual for the mvs found at KLOV - neo geo mvs and it didn't show any of those 10 hard dips as screen flip, nor any other mention of screen flipping.
I doubt that it would be the cart, unless there were special carts that had flipped video output for some reason (that I've never heard of, but also never checked into). Is it a USA mobo/cart? (don't know if that even matters).
Rick