The alarming figure on the charter school reimbursement is the one under "revenue" here:
That's $546,247 less than we budgeted for FY16 for reimbursement. Note, though, that the FY16 budget as passed in June still did not budget for full reimbursement (based, as it was, off of House 1). This the final total is about 69% of what state reimbursement should be.
Note this from the "tuition assessment" lines:
That $47,361 is an increase in funding going to the local charter schools. It should be reflected in the above "Revenue" line.
But, instead of the revenue line increasing, as the reimbursement calculation calls for, it instead falls by over half a million dollars.