Some come to the treasurer's office in person, but increasingly most pay online.
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Those paying online were routed to the Chase Bank site that was experiencing technical difficulties the last 24 hours.
A spokesman for Chase confirms the site was down for two hours Wednesday morning and Thursday is was running slowly for some time.
Chase released a statement saying: "The site is running, though some pages are slow to load. We're working to fix that and encourage taxpayers to keep trying."
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Jonathan Mraunac didn't want to risk paying penalties if his payment was late, so he came in person.
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"I got an error once I got to the payment page. So I tried again, maybe ten times, and kept getting the same error. And then I tried it again this morning and that's why I'm here," he said. "They encouraged me to try it one more time because Chase had fixed it, so I did."
"We had a glitch this morning, which was a minute and a half delay on processing payment. So we have overcome the glitch, having talked with Chase in New York," said Cook County Treasurer Maria Pappas.
The Cook County treasurer said despite the glitch, the today's deadline remains.
"There is no reason to extend anything at the present time, no reason. If someone has a problem, the email, the phone system is up. We are going to accommodate everybody," said Pappas.
Chase said the site was working as of Thursday afternoon. Taxpayers have until 11:59 p.m. Thursday to pay their bills.