While overseeing Guantanamo, he blocked attempts to get a commander of the camp reprimanded over abuse claims.
Caseworkers had not fully investigated one abuse claim.
In March 2013, the school was reportedly in negotiation with more than thirty students for compensation relative to the abuse claims.
Key to that decision is whether the judge believes the sexual abuse claim.
Ms. Lynch said about 100 additional abuse claims were pending.
The group processed over 470 abuse claims.
Some lawyers for the victims said the settlement, like those before it, reflects a changing attitude among church leaders, who once bitterly contested abuse claims.
Last week, Justice Stackhouse said the elder abuse claims had not been substantiated.
However, conflicting reports from the World Health Organization, made public in 1991, dispute the abuse claims.
A wide range of abuse claims were filed in a federal lawsuit in March 2012.