When applying Multi Seal to a floor already impregnated with a sealer such as MN Stain Stop, especially if it is a smooth honed floor, there are a couple of tricks.
You must get the first coat of Multi Seal to go on evenly. If it beads or becomes streaky try rubbing a very thin coat into the stone with a cloth or a green kitchen scouring pad (don't scratch a soft stone). You only need wet the stone and apply a very thin coat like this. The next 2 - 4 coats will be very easy to apply.
If this still doesn't work wash the floor with a failry strong solution of Lithofin Wexa first. Rinse well and allow to dry. Multi Seal should now go on much more easily.