Jona Bronson, 30, of Tillamook, said the children's father, John Eckhart, who lives in Vancouver, Wash, arranged a visit in Portland with Bronson, who had not seen the boys, aged 5 and 7, since April 2010.
"They don't really respond to people," she said of her sons. "They seemed fine. Their hair was dirty, that was the only problem. I thought they were potty-trained.
"I don't have a very strong relationship with them right now," Bronson told the Portland Oregonian. "He has kept them from me."
Still, she said, she believed the children were in school and being cared for by their father and his fiancee.
Eckhart, 30, and his 26-year-old partner, Alayna Higdon, were arrested Tuesday and have been charged with second-degree criminal mistreatment charges for allegedly boarding up the two children in a bedroom of their Vancouver apartment.
Police say the bedroom door had been replaced with a cage-like door.