District officials said they recognize that there are challenges that have caused charters' autonomous structure to clash with district-wide initiatives.

"It's a major source of conversation, and it's an ongoing challenge, and we're trying to think of different ways of representing charters in all of those conversations," Perkins-Cohen said. "The balancing of delivering on our commitments and giving them autonomy at the same time is a work in progress."

Among the longstanding challenges charters have faced is the funding it receives from the school system.

Under Alonso, all schools receive funding based on a per-pupil model. The charter schools receive a higher per-pupil allotment than traditional schools every year, because they are paid cash in lieu of services that they do not receive from the school system, like food and facilities.

School officials have also said that the charters' growth has become a financial burden to the school system.

But, school leaders say, the formula is interpreted differently every year — state auditors found that the district actually shorted charters in 2010 per-pupil allotments — and their per-pupil funding has been affected by the district's rising costs, particularly in the areas of transportation and special education.

School system officials are in the process of assessing where costs of services can be trimmed and developing a "fee-for-service" program that would allow all schools to opt into the services they receive from the central office.

"It's been difficult," Perkins-Cohen said. "But it's been a priority for us, to understand the differences between the formulas."

And the state charter law, which is recognized nationally as one of the weakest, may be revisited in the legislative session to help flush out many of these issues.

"We won't be able to survive and thrive if we have contracts and policies that affect us disproportionately," McKenna said. "We're definitely thinking about the next 10 years."