I think what's happening with your buns is that in the beginning, they were still a bit timid and scared about their new territory. Now that they have gotten used to it and settled, they are more comfortable and can go around marking what's theirs.
Have you tried using old, or new, carpet squares where your rabbits can mark their territory? You can cut 12 by 12 inch pieces and place them strategically around the room, or wherever else they are leaving...presents.

You could also watch them like a hawk, and before they have a chance to pee, scoop them up and place them in their litter box. Good luck!