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The State Auditor's office made the kind of request that state employees -- or employees of any kind -- likely don't hear very often: go ahead and gripe.

State Auditor Beth Wood's office is examining the state's BEACON (Building Enterprise Access for Core Operation Needs) payroll system, now legendary for its glitches, and is asking state employees to anonymously report problems they have experienced.

"Reporting a BEACON issue will help our office focus on areas where BEACON may need improvement," wrote Lisa Outlaw, a supervisor at the auditor's office.

State officials installed the BEACON system for processing paychecks early last year, and state employees since have complained of a parade of mistakes, including paychecks that were too small, missing numbers on tax forms and a help desk that wasn't, well, helpful.

State employees checking their W-2 forms last week found some of the numbers out of whack.

It was another attack of the BEACON payroll system.

A box that was supposed to have numbers in it, one showing the amount of pre-tax money set aside for dependent care was blank, while a box for distributions from a retirement plan should have been blank had numbers in it, Lynn Bonner reports.

Sherri Johnson, spokeswoman for the state controller's office, said the mistakes found their way into 17 percent of employee tax forms, or about, 17,000.

The office sent notes to state agencies' human resources and payroll departments, and to employees with computer access who log their own time, saying new W-2s were being printed and delivered.

It took two employees a day to fix a "configuration switch" that was not set correctly, Sherri Johnson, spokeswoman for the state controller’s office, wrote in an email.

Johnson made a point of noting the old payroll system had its problems with W-2s. About four or five years ago, all W-2s from central payroll put “deceased” in the employee boxes, Johnson wrote, and all the forms had to be reprinted.

Turns out the number of state Department of Transportation employees who were shortchanged on their pay today is larger than officials first thought.

State Controller Robert L. Powell says that 407 employees missed out on a total of $288,954, Pat Stith reports.

To make up for that checks will be delivered this afternoon to employees who work in the Raleigh area, he said. Checks for other employees will be delivered Saturday to a DOT facility where they can pick them up.

That's faster than depositing the money directly in their bank accounts, Powell said.

He said the underpayments, totaling a week's pay for many of the employees, was due to a human error made while the payroll system was being "tweaked" to fix something else.

Powell, whose agency is responsible for the payroll, said he would apologize to the employees who were not paid in full on time.

"It's a new system," he said. "It just happened. We're fixing it."

Several hundred employees of the state Department of Transportation weren't inadvertently short changed today.

"It looks like about 250 people only got half of their check," State Controller Robert L. Powell said.  "Right now we're trying to identify what happened, why it happened, and we're preparing  another payroll today to make those people whole."

Powell's agency operates the new "Beacon" payroll system. Pat Stith reports. He said there had been relatively few glitches since it was installed at the DOT last December and gradually extended to other state agencies.

Powell thought today's problem was an anomaly.

"I don't really know know why it happened," he said.  "What I do know is we're going to make those people whole today."