Last week, Brian Flaherty found himself in a long line of taxpayers at the City Hall Annex.

But, unlike most waiting, Flaherty wasn’t there to pay his taxes. Rather, he was trying to prove he paid taxes on his car. He said tax collectors didn’t want to believe him, even after he returned with a copy of his bank statement showing the check he sent in July. He was required to come back with a copy showing both sides of the canceled check.

Flaherty isn’t alone.

A frustrated Jim Chicoine stopped into Beacon offices to report he had stood in line on three occasions to clear up his taxes. He produced a copy of a check for $112.45 for his GMC truck that had been marked as paid to the city on July 17, 2013.

“They wouldn’t accept it, that I had paid my taxes,” said Chicoine.

Chicoine, a Marine Corps Vietnam veteran, said he returned with a copy showing the front of his canceled check. He was told to come back with a copy of the other side of the check, which he did.

He said at that point he was told there was an outstanding balance from December 2011 and the money would be applied to that. He questioned how he could be delinquent on his 2011 taxes without receiving notice last year.

“When they checked back then and I didn’t owe taxes, why am I not good now?” he asked yesterday.

Asked if the matter is straightened out, Chicoine, who said he has PTSD and is 100 percent disabled, said he left the tax collector’s office before resolving the matter.

“Before I blew up, I came to you,” he said.

According to a representative in the tax collector’s office, the Department of Motor Vehicles ran a list of delinquent motor vehicle taxes last October that is then forwarded to the city. Those blue notices are then sent out in waves after the first of the year and tax payments must be current in order to register a vehicle.

As to taxes owed by Chicoine, the department has a record that he paid $277 in cash on Dec. 27. There is no record of an amount of $112.45 as outstanding, or having being paid. In the case of Flaherty, the department showed payments of $202.33 to date and $91.08 as being owed.

City Treasurer and Tax Collector David Olsen said Tuesday there had been an issue with the data provided by the Department of Motor Vehicles. He said the information was keyed to the registration plate so that, when the plate is transferred to someone else, the payment isn’t properly applied. He estimated this might have happened 50 times but that steps have been taken to correct the problem.

“We’ve changed the software. We’ve taken care of that,” he said.

Neither Chicoine nor Flaherty recently registered, or changed registration, on their vehicles.

Informed that at least two taxpayers were told they hadn’t paid, even though they produced canceled checks, Olsen said, “That’s not true.”

He said when people claim to have paid taxes, “We ask for proof of payment. We verify the payment.”

Olsen dismissed the possibility that Flaherty and Chicoine’s cases might be linked to the lock box system implemented last July.

“That’s been beautiful,” he said, “we have money in the banks.” Under the system, city tax and utility payments are now sent to a Massachusetts address, were they are promptly deposited in city accounts and the records forwarded to the city. Prior to the lock box arrangement, the city processed all payments. In some cases, checks were not being deposited for several months at a time.

With the acceleration of processing payments, Olsen said the city is becoming more vigilant in posting interest on non-payments. He said the “grace period” for quarterly payments due Jan. 15 will end at the end of the month. On the next quarterly payment, which is due April 15, he said the grace period would be reduced to one week.