The Small Business Administration is behind schedule on five of six planned improvements to its Loan Management and Accounting Systems and costs for the overall project have risen about 20 percent since 2010 to $28 million, a recent Government Accountability Office report said.

That’s a common story with federal information technology acquisitions, which often run behind schedule and over budget. President Obama’s planned consolidation of SBA with several other business and trade agencies inside the Commerce Department could throw another cog in the wheels.

Major government reorganizations have a mixed track record of success, but one common feature, experts told Nextgov, is while the reorganization is in process, uncertainty rises.

“Often the [reorganization] process takes a lengthy period of time and during that period it’s difficult to deal with real issues and challenges in the agencies,” said Alan Balutis, a former chief information officer at the Commerce Department and now a director at Cisco’s Internet Business Solutions Group.

“It’s almost like you bifurcate staff and resources,” Balutis said. “One group works on the reorganization and integration and another group goes along doing their daily business and waiting for the day when someone pulls the switch and everything changes.”

During that transition period problems that already exist with a project or system can “linger and fester,” he said, because employees managing the project are unsure where the system will fit in the new organizational structure. Often those staffers also are unsure where they’ll fit in the new structure and, as a result, hesitant to make major decisions, he said.

“They’re working under uncertainty about ‘Where am I going to end up? Who am I going to be working for? How is this going to affect my grade and responsibilities?’ ” Balutis said. “And all of that is a distraction when you’re trying to carry on your regular duties.”

That’s not to say all acquisitions and projects will fare equally poorly during a bureaucratic transition.

“If you have [information technology] systems that are more enterprisewide, that support an agency function like, say, supply chain management or finance, those are likely to be more affected by reorganization,” said Raj Sharma, president of the Federal Acquisition Innovation and Reform Institute and author of a report on IT acquisition reform.

“If you’re looking at a mission-specific system, something that supports a critical program but we know it won’t be affected by reorganization, then there’s a higher degree of certainty,” Sharma said.

Programs also are less likely to fall into reorganizational paralysis if they’re being closely monitored by government leaders or the public, Sharma said.

That may bode well for SBA as Obama and Republican House leaders have spoken at length about the importance of small businesses to an economic recovery.

GAO’s review of SBA’s loan system was performed from February 2011 through January 2012, almost entirely before Obama announced his reorganization plan, Jan. 13. That plan will require congressional approval to be enacted, which may be tough to come by. It also involved elevating SBA to a Cabinet-level agency while the transition is in process.

A GAO spokesman declined to comment Thursday on how the proposed reorganization would affect problems with SBA’s Loan Management System saying it was beyond the scope of what the agency had looked at.

In its report, GAO criticized SBA officials for failing to validate that certain technical requirements had been met and for not identifying potential risks or taking steps to mitigate them. The agency also didn’t identify skills gaps on the project teams and didn’t get firm baselines from all contractors for how long the projects would take, GAO said.

“These weaknesses in basic management practices make it less likely that SBA will be able to complete the projects within the time, budget and scope parameters originally planned,” GAO said.

While Balutis is skeptical that major problems will be solved during the proposed SBA-Commerce reorganization, he supports the reorganization itself, which he said has been discussed for years in different forms. If done right, he said, the reorganization could save money and create useful cooperation between SBA and some units of Commerce that do similar work, such as the Minority Business Development Agency.

Balutis is cautiously optimistic that the reorganization can win congressional approval.

“There certainly hasn’t been much the White House and the Republican-controlled House has been able to agree upon over this last year and a half and probably the range of issues on which they agree is only going to narrow as we roll up to the election in November,” he said. “On the other hand, this does seem to strike the right chord. One thing a number of people agree on today is that we ought to rationalize the government. We ought to make it smaller and tighter to achieve savings. And that was a major premise of the White House announcement.”