In an era of tight credit and swift punishment for payment delays, several glitches in personal finance software are making it difficult for some customers of major banks to pay their bills on time.

As banks are developing their own online bill-pay systems and the popularity of free online personal-finance-management, or PFM, services like Mint.com and Wesabe.com grows, consumers who still use a third party s software have been reporting customer-support problems that industry analysts say the banks may not be in a hurry to resolve.

Over the past several weeks, (JPM) customers have been reporting problems when attempting to pay bills from their Chase accounts using (INTU) Quicken software. Others have reported errors that prevent the software from updating their accounts. Reports date back to mid-October, and for some users, the problem persists.

John Rivard, a Chase customer and Quicken user, says he has been unable to pay any bills through Quicken since mid-November. In every one of his conversations with Chase customer service, Rivard says he was told the bank is working on the problem but does not know when it will be resolved.

The interim solution Rivard has been offered: Use Chase s own online bill pay system, which Rivard says isn t as sophisticated as the Quicken software he is used to. He isn t able, for example, to split one monthly payment to his phone, cable and Internet provider into three separate categories, and automatic bill payments on his auto loans and mortgage now have to be entered manually. It is an inconvenience, yes, but a pretty significant one in terms of time wasted, he says.

Christine Holevas, a Chase spokeswoman, says that Chase has worked with Intuit to resolve the issue for most customers, but because many people customize their software, a small amount of individuals continue to have problems. The company is working with them to resolve their unique problems. Quicken says the issue is with Chase s systems and was a result of the transfer of accounts from Washington Mutual, which the bank acquired in September 2008 in a deal brokered by the Federal Deposit Insurance Corporation that was designed to save the bank from collapse. Intuit says it will work with Chase to resolve the problem.

Industry analysts say that although incidents like this are not very common problems typically get resolved behind the scenes before the user even finds out they highlight a larger trend in the industry. There s certainly a strong preference on the part of the banks that you do all this activity on the bank site and not a third party, says Emmet Higdon, a senior analyst who covers online and mobile financial services at market research firm Forrester Research.

Quicken and MS Money initially may have revolutionized and automated the way consumers manage their finances, but now most people are migrating to online banking directly from their bank or through a free online service like Mint.com. The scenario of someone doing bill pay through Quicken or MS Money is very much a legacy of the online bill pay space, Higdon says.

In a recent Forrester Research survey, 75% of the respondents said they would prefer to get the functionality of a PFM service directly from their bank or credit union, not a third-party provider. And banks are attuned to that sentiment: Most of the top 20, if not the top 50, banks in the country are now working on an in-house PFM solution, says Higdon. He says he expects that the majority of the top 20 banks will offer some kind of PFM functionality within the next two to three years.

So while an online bill payment error with a third-party provider like Quicken should be an easy problem to fix, it may just not be that much of a priority for a banking institution that is hoping to direct more customer towards its in-house solution, says Nicole Sturgill, a research director at market-research group TowerGroup. The fix will be a different way of doing [bill pay] rather than being able to do the same thing you were doing a month ago, she says.

Of course, winning customers that way is a risky proposition. The consumers who use Money or Quicken tend to be more affluent and they also tend to be very engaged with managing their money, says Ron Shevlin, a senior analyst who covers retail banking at market research firm Aite Group. These are the folks that are most engaged with the bank and their financial lives although they represent a relatively small percentage of the total online banking population," he says. "The bottom line is this is not the group you want to push off because they tend to be your best customers.

As for the future of its boxed software, Intuit has seen the writing on the wall. In September, the company acquired Mint.com, which over the past two years has attracted 1.8 million users, according to Aaron Patzer, the vice president and general manager of the personal finance group at Intuit. That s still just half the number of Quicken's 3.5 million to 4 million users. But with the company reporting 120,000 to 150,000 new users each month, Mint.com appears to be closing the gap.

And even though (MSFT) has already announced plans to discontinue production and support for its MS Money box solution, Intuit plans to retain Quicken as an independent service. But the product is about to get mintier. Next year, the company will integrate within Quicken the Mint.com Ways to Save feature that looks at a consumer s interest rates and investment and savings yields and scours the web for better offers.

It s the kind of thing a bank will never do for you because it is pushing its own products, Patzer says.