A lot of kitty moms will move a litter when a threat is perceived ... where do you have the box located? Is it in or near a high-traffic area? Do lots of people go by the box frequently or is there a high activity level nearby?
How about the nesting material ... is it fresh? If Momma thinks it is soiled, then she will move the babies to protect them. Is the box too near to the litter box or food bowls? If so, move the litter and food to a location further away from the nest so Momma is more comfortable and won't move them. Keep the box pristine at all times and promptly remove any stale food. Make sure water is fresh and clean at all times.
What about the temperature of the box location? It is in a drafty, cool place or could it be too warm? Lighting? Too bright? Kitty moms like a warm (but not too warm), dark, nest-like place to raise their babies.
At two weeks old, Momma may also be moving them out of the nest so that they can begin to stretch and use those little leg muscles. You could probably allow that a bit but use caution ... kittens can move faster than you think and they can get into places you would never dream they could fit into. Block off any dangerous places, close closet doors, secure any openings to under the bed or vents. While it is nearly impossible to completely "kitten-proof" a room, get down on the floor and look around at their level. Even if something doesn't look interesting to you, it will look interesting to them.
If she keeps on moving them, my suggestion to you is to get an extra-large dog training-type crate. They are roomy enough to accomodate a growing family of cats along with food and water dishes, a small litter box and bedding. They don't have to be in it all the time, just when you cannot supervise their activities and don't feel comfortable letting them roam.
Hope this helps,