TD Bank officials say there have been delays in getting transactions to show up in the customer's accounts.
They say the problems sprung from complications integrating the computer systems and Web sites last weekend of the old TD Banknorth and Commerce Bank.
In the days just a few years ago before online banking was not widespread, most customers would not have noticed.
But now, they're so aware that they've overwhelmed the phone lines at the bank's call center, filled branch lobbies and have made their gripes public on Twitter.
"We recognized the frustration level was increasing during the week," said Fred Graziano, who was contrite about the problems.
The lingering problem was compounded by the timing.
With the first of the month followed by a Friday, Social Security, many pension payments and paychecks were to be deposited.
And many mortgage payments were to be withdrawn.
Graziano said the deposits and payments have been going through correctly.
But people could not see that they were by logging on to the bank's Web site.
Colleen McCarthy, who lives in Brooklyn and works in public relations said she was nervous Tuesday, when her paycheck was to be deposited and her car and car insurance payments were to be deducted.
The Web site did not show any of those transactions Tuesday, or Wednesday.
"It showed my balance as being $100," she said.
And when she called customer service, she got a message that the line wasn't in service, making her fear her bank was going out of business.
"The net-net is, my paycheck finally got deposited or credited yesterday," she said as she visited the bank's Web site Friday. "I still don't know if my car payments or car insurance got made."
Guy Fardone, chief operating officer of Evolve IP, a technology services company in Wayne, Pa., said these kinds of problems are common when companies merge computer systems. But he said usually they frustrate only the employees.
In this case, it's a problem for customers, too.
Graziano said TD has been making headway at fixing the glitches - and has added more lines into the call center.
The bank is also ensuring customers that it won't charge any fees because of the glitch - and that it will reimburse fees that other banks charge because of it.
Graziano said there should not be many of those because payments and deposits are going through.
He also said bank managers were depositing $25 into the accounts of some upset customers as a way to compensate them for their troubles.
TD Bank was created last year after Toronto-based TD Bank Financial Group bought Cherry Hill-based Commerce Bancorp, a retail-focused bank that developed a cult following.
The combined bank has headquarters in Cherry Hill and Portland, Maine, more than 1,000 branches between Maine and Florida and some 6.5 million customers.
Though the brands were consolidated nearly a year ago, the computer systems remained separate.
Jim Galvin, a film industry dimmer board operator from Union City, N.J. said he wasn't surprised by the technology issues.
"Things have changed and they've really changed for the worse," he said.
Associated Press reporters Damian Grass in Doral, Fla., and Clarke Canfield in Portland, Maine, contributed to this article.

That's the trouble with big companies they grow too big, but their logistics are deficient. That's why I switched all my business to Credit Union.
Small town banks are the best! I love Franklin Savings!
so glad we switched to a CU when TD BankNorth got rid of free checking and free savings this summer!
Yes, that was really a case of bait and switch, and we left TD as quickly as possible. They have spent years trying to get their act together while they merge and merge into a larger and larger bank, and still have not caught up with the small fries like the CU and Bangor Savings Bank (where we fled) in terms of the functionality of their web banking and the personalization of service.
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