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Why does this keep happening to IBM?

A sign marks the entrance to IBM Corporate Headquarters in Armonk, New York.
Stan Honda | AFP | Getty Images
A sign marks the entrance to IBM Corporate Headquarters in Armonk, New York.

IBM's struggles evidently go well beyond technology.

For the second time in a little over two years, Big Blue faces an investigation into how it records revenue. The company disclosed on Tuesday that the SEC is looking into the "accounting treatment of certain transactions in the U.S., U.K. and Ireland."

The stock dropped 4 percent to $137.86 after the revelation and was down 14 percent for the year at Tuesday's close before bouncing back a bit Wednesday morning.

IBM said it learned of the probe in August, but it said little else about the inquiry. With no more detail, it's hard to know exactly what's causing the confusion.

Last time there was a little more clarity. The Armonk, New York-based company said in mid-2013 that the SEC was investigating "how IBM reports cloud revenue." Ultimately, IBM avoided any enforcement actions.

A spokesperson didn't respond to an e-mail asking about the nature of the latest investigation, but the company did say, "We are confident that the results and information we report have been appropriate and consistent with GAAP," or generally accepted accounting principles.

IBM shares

Why has accounting all of the sudden become such a challenge?

At least as it pertains to the shift to the cloud, the change is not just about technology, but about business model.

In the old world, software and hardware products were bought and sold. Multimillion dollar licenses were paid upfront spanning several years, with maintenance fees tacked on annually.

Read MoreWall Street's ongoing struggle to make sense of the cloud

It doesn't work that way in the cloud. Clients pay for subscriptions, often writing checks monthly or quarterly. Revenue gets recognized over time. Renewals happen because customers like the service, not because they're locked into proprietary systems. In the universe of Web applications, this is generally called software as a service (SaaS).

"Software is an area where revenue recognition can go one of two ways," Charles Bobrinskoy, vice chairman of Ariel Investments, told CNBC. "The same exact deal can get treated as a license or as a subscription and the accounting is very different."

IBM, like mega-cap tech companies Microsoft, Oracle and SAP, is slowly shifting from the old to the new, as businesses demand the efficiency, speed and advanced analytics that come with collecting their data in the cloud.

For IBM, this is mostly happening through acquisitions. Since the beginning of 2011, IBM has bought at least 40 companies, including retail analytics provider DemandTec, cloud infrastructure vendor SoftLayer, cloud marketing platform Silverpop and just last month StrongLoop for mobile application development.

Cloud revenue at IBM reached $9.4 billion in the past year, representing 11 percent of total sales. IBM said that within the cloud business, it's on pace to generate $4.5 billion of annual "as-a-service" revenue, up from $3.1 billion a year earlier.

Still, investors haven't had much to get excited about, with IBM reporting quarterly revenue last week that missed even the most pessimistic estimates and its forecast also coming in below expectations.

Accounting issues are just adding to the pain.