If milk kefir keeps separating most f the time the means that milk grains to milk ratio is too high. Or the temperature of fermentation is too high.
Try removing some grains or add more milk to balance grains to milk ratio is 2 tablespoons of milk kefir grains to 1 quart of milk.
Otherwise with higher kefir grains to milk ratio the separation will proceed faster and it could be difficult to catch the right time when to strain milk kefir.