GSD's odd reaction to temporary addition to household?

I adopted a 2 year-old GSD from a rescue organization about 5 months ago. She has adjusted well to the family and is in all ways a fabulous addition to our family. I started providing childcare for my sister's 1 year-old son, who is really great with our dog and has one of his own at home. The only oddity about my situation is that after my nephew leaves in the afternoon, my pup doesn't want to go outside to go potty. The first day he was here, she actually peed a bit in the house when we asked her to go outside. I'm sure it's got to be a position-in-the-pack kind of thing, but how can I help? She's fine when he's here, very watchful, sniffs him when he falls, overall she's very caring. I just don't want my little pup to feel she has lost her place in our pack. Any ideas?