After years of problems, Seattle Public Schools is on track to fix most special-education issues the state has identified. The School Board will vote Wednesday on whether to approve a new oversight agreement that could open the door to $3 million in withheld federal money.

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Seattle Public Schools’ long-troubled special-education department is making headway toward regaining millions of federal dollars withheld for the district’s failure to educate children with disabilities.

Of the 40 compliance problems the state has ordered the school district to fix, 39 are resolved. The district has a new, 275-page special-education policy manual, has hired an ombudsman to field parent complaints and is planning more training for its special-education teachers.

The department’s new leader, who took over in August after the former director was put on administrative leave, said he and all his employees are planning to return this fall — a big change for a department that has seen nine directors in about six years.

But some parents say they have not seen the progress they hoped for, and the Seattle Education Association says special-education teachers are still aching for support.

“As they (at the district) have been concentrating on these compliance issues, the classrooms are actually falling apart,” said Phyllis Campano, vice president of the teachers’ union. “There’s so much to do, and not a whole lot of support.”

Cecilia McCormick, a parent and treasurer of the Seattle Special Education PTSA, said despite the district’s progress toward a more organized department, parents haven’t seen improvements in classrooms.

“And that’s what matters to us,” she said.

Still, the district seems to be moving in the right direction, said Doug Gill, special-education director for the state Office of Superintendent of Public Instruction (OSPI).

The School Board will vote Wednesday on whether to approve a new agreement with OSPI that stipulates less frequent oversight next school year. The agreement outlines what it will take to restore $3 million in federal money OSPI has withheld until the district can prove substantial progress, and to remove Seattle schools’ status as a “high risk” recipient of federal dollars.

For years, the state has urged the district to address problems in its special-education program, from failing to keep up-to-date student-learning plans to inconsistent delivering services to schools.

A district audit showed special-education student files missing signatures, outside services for students performed before contracts were approved, missing documentation for outside contracts, and the lack of a handbook clearly stating policies and procedures.

In August, then-executive director for special education Zakiyyah McWilliams was put on administrative leave while the district looked into the suspicious hiring of a special-education consultant. McWilliams resigned a few months later. An investigation found she violated district policy by emailing competitors’ bids to the consultant who won the contract.

Then, in October, the state notified Seattle Public Schools it would keep $3 million of the $10.6 million it was supposed to receive this year for special education. The department’s total budget is $103 million to educate about 7,200 students, whose needs range from learning disorders to autism to intensive medical problems.

Since then, the district has made big strides, said Wyeth Jessee, now the head of special-education services at the district.

Turnover is a root cause of the district’s compliance issues, he said. This year, Jessee’s goal is to fill 98 percent of all special-education positions before school starts. (Last summer, the district had 45 openings for special-education staff when school started, he said. They year before had 80.)

He plans to hire teachers early and train them more, all in the hopes of ultimately steering the focus beyond compliance to better student outcomes. The district hired a special-education recruiter and is working with the University of Washington and other colleges to find new teachers.

“We’ve gone out to every job fair,” he said. “We’re shaking hands. We’re making phone calls.”

The new policy and procedure manual is a model for the state, he said.

“I’ve got calls coming from other districts, (asking), ‘Can we get a copy of it?’ ” he said.

OSPI has visited every week to check on the district’s progress. Once a month, the district and state hold three days of meetings to discuss the changes.

Under the new agreement, if approved, OSPI would begin a series of visits to Seattle schools over the next year. The state will study random samples of student files to make sure the district-level policy changes are being followed in classrooms. If, among other requirements, a certain percentage of those student files are completed correctly, the federal money will be incrementally restored.

Hannah Marzynski, parent to a son with special needs, said she’s impressed with what the district accomplished this year — though it should have been in place long ago. Marzynski, a member of the committee that advised the district on how to respond to OSPI’s concerns, said the district now has clearer outlines of who should handle what in special education.

“I am heartened by what has occurred over the last year with the new leadership,” said Jennifer Adair, head of the Seattle Special-Education PTSA. “They are really trying to change the system from inside out.”

Still, teachers are hungry for more help with special-needs students, said Campano, the union vice president.

Twice this year, she said, the union has activated a little-used section of the teachers’ contract to assemble a crisis-intervention team at elementary schools when special-needs issues got out of hand.

The School Board meeting begins at 4:15 p.m. Wednesday in Seattle Public Schools headquarters at 2445 Third Ave. S., in Seattle.