
Have you cut their nails yet? If so then it won't be discomfort. It has been warm so it could be she is to hot.
As long as she is in feeding and cleaning them at least every two hours and they are gaining well then lying outside the whelping box is normal.
To discourage mien from being away from their pups due to attachment to me I spend a lot of time in the area where the whelping box is so that she can be with them and me.