The charter school's nonprofit, led by O'Shea's wife, Jamie, has received more than $2.4 million in taxpayer funds in rent payments since 2005, state records show.
Investigators have been unable to locate all the nonprofit's records, and the membership of its board is unclear, according to school district sources and those involved with the charter's internal probe. Two people who were listed as being on the board said in separate interviews that they had never served.
The investigators also are looking into the possibility that the nonprofit used proceeds from the rent payments to invest in other properties, according to people familiar with the probes.
Henry E. Hockeimer Jr., a lawyer overseeing the school's internal investigation, said the rent payments to the nonprofit were "certainly an area of interest and concern."
The existence of the independent nonprofit has complicated the broader probe of Philadelphia Academy, which was founded in 1999 and with 1,200 students has become a major publicly funded school in the Northeast.
The Philadelphia School Reform Commission voted June 18 to grant the school a new five-year operating charter on several conditions, including severing all ties to Gardiner, its founder, former CEO O'Shea, their families, and all businesses and entities in which they are involved.
The deadline was Monday, but the nonprofit's status as landlord and the fact that it was created by Gardiner and run by O'Shea's wife have complicated matters. While the SRC has authority over the charter, it has no say over the independent nonprofit corporation.