Paul Mortimer knew he paid his taxes long before the quarterly payment was due on July 15. And having had a career that spanned more than 40 years in banking, he knows how a lock box works and that checks received are rapidly processed, often posted to the receiver’s account in 24 hours.

That speed in processing was the reason the city went to a lock box operation and why, when paying taxes and utility bills by mail, return envelopes carry a Boston address.

But by the end of July when Mortimer hadn’t seen his tax payment clear his account, he wondered where the system had broken down and whether, in fact, he might be faced with a late payment fee from no fault of his own. He called City Hall but he couldn’t get an answer.

He’s not the only taxpayer to have called with similar inquiries.

City Tax Collector Kyla Jones said Thursday the department has received numerous calls about checks that haven’t cleared yet. She reassured people won’t face interest charges until after Sept. 15, the deadline for those electing to pay their taxes in full even though this would be the first quarterly payment.

But why aren’t some payments, like Moritmer’s, clearing the system designed to expedite the process?

Jones offered a number of explanations ranging from the incorrect tax account number on checks – the numbers are not always identical from year to year – to combining utility and tax payments in a single check. Sometimes checks are sent without the tax stub and with no identifying number as to what is being paid.

Others disregard return envelopes with the address of the Boston processing center and mail payments to City Hall. Still more make payments through online banking and at the counter at the City Hall Annex.

This year was no different than years past with lines stretching out the door as the July 15 deadline approached. But there have been substantial changes since the days – not that many years ago – when the tax collector’s office processed all payments. As the first quarterly payment approached, personnel from departments throughout the city were reassigned to cope with the wave of payments. There are a lot.

This year, the city issued almost 50,000 motor vehicle and 43,000 property tax bills.

Even with the added help, the city wasn’t capable of processing all the payments in a timely manner. Some July payments weren’t being processed until that fall and people were questioning if the city had received money as the second quarterly payment came due.

Former City Council President Bruce Place along with Mayor Scott Avedisian pitched in one year to open mountains of envelopes in hopes of expediting the process. Former City Treasurer David Olsen introduced the lock box, which immediately stepped up processing and tightened the system. It also improved cash flow.

“It’s moving a lot better than it was years ago,” said City Finance Director Ernest Zmyslinski. There have been some changes although that shouldn’t be noticeable to the public. Based on bids, the city has switched banks from Citizens to Webster Bank. Webster subcontracts lock box operations to Fidelity, as did Citizens, so that remains the same.

Zmyslinski said Webster “aggressively pressed” for the city business and their bid made it worthwhile to change banks.

Jones noted those choosing by pay through their online bank account may also question if their payment has cleared. She explained the bank issues a check so while the payer may assume the transaction is completed, the city needs to receive it and deposit the payment to complete the process. Payment by credit card is also an option, but there is a 2.5 percent surcharge of the amount or $3.95 [whichever is greater] that goes to a vendor that handles processing and submits the tax payment to the city.

The city billing totals $233.3 million, which when broken down amounts to $24.6 million in motor vehicle taxes; $21.3 in personal property and $187.4 million in real estate.

Jones urged taxpayers to include their account numbers on their checks and include tax stubs with payments. As for those having difficulty making payments, she recommended they contact the collector’s office and establish a payment plan to avoid incurring additional expenses and perhaps even eventual loss of the property should it go to a tax sale.

“Once you fall behind it’s hard to play catch up,” she said. Presently, 195 taxpayers are on a payment plan.

On Thursday Jones was faced with ten trays of checks “in the holding cell” that needed to be paired with taxes due and credited to accounts.

Supposedly, Mortimer’s payment was not among them.

He reported last week that the collector’s office told him they had processed his check on Wednesday. Yesterday he called to say his check still hadn’t cleared, so he is mystified.

Mortimer used one payment to pay taxes on three parcels of property. He included stubs for taxes on each of the parcels.

Those concerned whether their payment was been properly accounted for can go to the city website and check their account information using their last name to search the database. The information is public record and accessible to anyone.