Raleigh, N.C. — Problems afflicting the state's payroll system should be resolved, the state controller is telling legislators.

In a letter Friday, Controller David McCoy reported to the General Assembly on the troubled Beacon system, which processes paychecks for nearly 90,000 state workers.

For almost a year, state employees have complained about paycheck errors, including wages coming up short and being overpaid.

Those problems were linked to a number of errors dealing with benefits, overtime and differential pay. McCoy said the issues had to do with data and encoding problems, as well as input errors. The office went through all employees' records to make sure they were coded correctly.

As of Friday, those who were owed money will have received it in their most recent check. More than 5,000 employees who were overpaid, had that amount deducted, McCoy said.

McCoy said his office notified state departments early this month about the fixes and said it was up to each department to notify its employees.

Those who had money deducted from their paycheck Friday can go to their human resources department and request an advance and then pay the money back over 10 months or have a percentage deducted from checks each pay period until it is paid off.

"We're required by law to recover those funds, but we also recognize there are families that receive those monies, and we don't want to impose a severe handicap on them. So, we are working with the agencies," McCoy said.

The state signed a $28 million contract in 2006 to replace a 30-year-old human resources and payroll system. After the cost grew to $71 million and the system had gone through an initial testing phase, Beacon was rolled out statewide in April.

Between December 2007 and August 2008, the Beacon call center received more than 64,000 questions and complaints from state employees.