Meat inspector Alfreda Dennis-Bowyer was looking forward to getting a paycheck — finally. She’s a U.S. Agriculture Department employee in Delaware with four decades of experience, and during the 35-day partial government shutdown she stayed on the job, working overtime, even though she wasn’t getting paid. When the shutdown ended, she expected to get all her back pay in a lump sum — about $9,000.

Instead she got a check for $250.

“When I saw that $250 I thought, ‘What in the world is this? Where’s the rest of my money?’ ” said 63-year-old Dennis-Bowyer. The underwhelming check turned out to be a reward for working through the shutdown. Because of glitches with the USDA payroll system, she didn’t get her full back pay until Wednesday, nearly two weeks after the shutdown ended. About 120 inspectors are still waiting.

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They are among thousands of employees who have experienced delays or anomalies with paychecks at the federal agencies that went dark. Many say they initially received half of what they were owed after working without pay or being furloughed. Others were stunned by what appeared to be excessive tax withholding. And some — the exact number has not been provided by government officials — had received no pay as of Thursday afternoon.

The paycheck situation is just one of many challenges and headaches for federal agencies and hundreds of thousands of employees attempting to restart the government. They are holding their breath, knowing they might have to endure another funding lapse in a matter of days if congressional leaders can’t strike a deal over border security. The nine Cabinet agencies and dozens of smaller ones affected by the recent shutdown are funded only through Feb. 15.

Republican and Democratic negotiators have said they might reach a compromise funding package by the end of this week. The last time the funding issue seemed on the verge of a bipartisan agreement, back in December, President Trump pulled the plug amid pressure from hard-liners in his political base. If Trump blocks a new deal, Congress could override him. Otherwise, large parts of the government could shut down again.

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Government experts said the many troubles with the restart, such as the payroll glitches, shouldn’t be a surprise. As a rule, the federal government can’t be turned off and on like a reading lamp. The funding lapse that began Dec. 22 caught many agency officials off guard, and the 35 days of the shutdown had a chaotic and improvisational quality that probably contributed to the chaos of the restart.

Simply signing on to an agency’s computer network proved difficult for many people returning to work, because their passwords expired during the shutdown.

Private contractors have also had to surmount bureaucratic hurdles. Some contracts expired during the shutdown. That happened, for example, with the contract for handling Freedom of Information Act requests at the Department of Housing and Urban Development, said attorney Ethan Bodell, who handles such requests. He said the contract hasn’t been renewed, and as a result, the office can’t get working on new requests or access its database of existing ones.

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Private contractors are also drumming their fingers waiting to be paid for work done months ago, said David Berteau, president and CEO of the Professional Services Council, which represents members of about 400 companies that do business with the government.

“Old invoices have not been paid. New invoices have not been paid. The first thing that should have been paid were old invoices that were actually for work done last October and November,” Berteau said.

The paycheck problem cropped up in the National Finance Center, which operates out of the USDA and runs the payroll for many of the government agencies affected by the shutdown. The center was given only a few days to process two full pay cycles for more than 600,000 employees, and had to modify its systems to process 1,343,456 disbursements totaling $5 billion in gross salary, USDA spokesman Tim Murtaugh said.

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The computers balked.

“Unfortunately, processing such a large quantity of payroll disbursements in such a short period of time resulted in 3,908 employees who received payment for only one pay cycle, and 7 did not receive any pay,” Murtaugh said in an email.

Those numbers do not jibe with anecdotal reports from employee union representatives and from interviews with government workers, which suggest that the number of people underpaid or not paid at all is much higher.

Many of the 450 Internal Revenue Service clerks who process tax transcripts for the lending industry in four offices across the country were not fully paid, according to interviews with employees and the National Treasury Employees Union, which represents them. The clerks spent about two weeks on furlough during the shutdown before the Treasury Department, under pressure from the industry to continue producing a key document essential to getting a mortgage, brought them back to work.

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The IRS said late Thursday that “a few hundred” employees had received “some but not all” of their back pay, and the remainder is expected to be paid over the next few days.

There’s another hidden cost to the shutdown: overtime pay. For example, the IRS clerks have been working overtime trying to cope with a backlog of 100,000 tax transcripts that accumulated during the shutdown.

Federal employees fear they may have to endure another shutdown, said J. David Cox, president of the American Federation of Government Employees, which represents 700,000 federal workers. Restarting the government is a laborious process, he noted.

"Just getting time cards corrected, that will take months," Cox said.

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“The mood is pretty subdued now. People are fatigued by the shutdown. They’re demoralized to some extent,” said David Verardo, president of AFGE Local 3403, which represents more than 1,000 employees at the National Science Foundation and other agencies. “It’s hard to plan past February 15 not knowing if we’ll have to cancel activities again.”

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On a good day, with the government functioning normally, immigration judges face a daunting backlog of cases, and that became all the more challenging when the courts reopened on Monday, Jan. 28, said Ashley Tabaddor, a Los Angeles-based judge and the president of the National Association of Immigration Judges.

She said she has more than 2,000 cases on her docket and no opening on her calendar until late 2020. She returned to work to find boxes of court filings filling a reception area in the office building that houses the immigration court. She said Justice Department officials insisted that everyone go back to work and conduct “business as usual” even though Tabaddor said it would have made more sense to spend a couple of days ramping up, going through mail and newly filed court papers, and getting organized.

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The long delay in issuing paychecks and poor communication between the administration and federal workers have fueled resentment and anxiety as another possible shutdown looms, said Charles “Stan” Painter, a federal poultry inspector and chairman of the National Joint Council of Food Inspection Locals.

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“My phone has been ringing off the hook. It’s a mess,” Painter said.

Even when federal workers have been paid, the way the money arrived baffled many federal workers. For example, at the Census Bureau, workers who were furloughed — who stayed home throughout the shutdown — received all their back pay last week. But the workers who were called back to the office during the shutdown — and forced to work without pay — are still waiting for their money.

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Carmen Rottenberg, who runs the USDA’s Food Safety and Inspection Service division, said because of a glitch in payroll processing, inspectors who worked overtime didn’t receive their back pay on Jan. 31. Those who didn’t work overtime did get their back pay.

“It isn’t much, but we wanted to do something for those who didn’t get paid anything,” Rottenberg said. “I really hope this doesn’t happen again. It creates an incredible hardship on our employees. People shouldn’t forget that if they aren’t there, no meat, pork or poultry can be produced in this country.”

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