Very often a cat will do that when they do not feel their kittens are safe. They are tring to find a "safe" place for them.
Remember that they do not judge "safe" the way we do.
One of the problems of putting them in the bathroom is there is a lot of traffic in the bathroom. If different people are going in and out of their, that can be interpeted by a cat to be a threat to her babies, especially if its not a home the cat has grown up in. but is a fairly new one.
If there are other animals in the house, she could even be trying to protect or hide them from the others. And that scent is there, even if she can't see them.
If you can, try to find a place that not only can you limit how far they can go, but where there is little traffic, so the interaction is planned and quiet and uninterrupted.
Personally, I wouldn't keep a cat with kittens in the bathroom. I think there's too much traffic, too much light, and too much noise (remember, plumbing makes noise we become acclamated too, but to them it's new, and can be scary).