for what I can tell maya always had and still has a problem to display alphamaps in viewport properly when you have overlapping and combined geometry using alpha. this seems to be a sorting or z-buffer problem which means if the geometry is combined maya doesn´t know anymore which plane to render first. this results in flipping textures from back to front and and overall transparent geometry.
here´s a picture to show ->
everything starts and ends in the right place at the right time.