Southwest Airlines’ transition of AirTran Airways flights into Southwest service hasn't been all smooth sailing since the merger last year.

The gradual conversion of AirTran's large Atlanta operation is bringing Southwest some unusual challenges and in the latest round of ongoing flight changes, the airline is temporarily shifting some Southwest flights in Atlanta back to AirTran service.

The flights being shifted back to AirTran include service from Hartsfield-Jackson International Airport to Los Angeles, Chicago Midway, Phoenix, Denver and Las Vegas.

Part of the delay is due to rebranding -- repainting exteriors and redesigning interiors -- of AirTran’s fleet to the Southwest design. The first converted AirTran plane will be available for service this month, with several more expected each month.

And the carrier still lacks the capability to connect travelers between AirTran and Southwest flights, limiting its ability to fill Southwest flights with AirTran customers. and vice versa. Though the carriers had hoped to have connection capability by the first quarter of this year, it is now not expected until 2013.

Southwest spokesman Chris Mainz said the company is "looking at the networks and trying to offer the best possible schedule for each. In some cases, until we get to a point a little bit further down the road, it makes sense to transfer some of that flying from Southwest to AirTran."

All told, Southwest will operate 30 flights from Atlanta this fall, while AirTran will operate 163.

"It's just a terrible dilemma they find themselves in after not coming to grips with that IT [information technology] problem," said Port Washington, N.Y.-based airline consultant Bob Mann. "I would think that's just got to be a critically important issue to solve right now."

In markets outside of AirTran's main hub in Atlanta, Southwest's takeover of AirTran routes is proceeding as planned, as Southwest gradually converts more AirTran planes.

"It sounds to me like they're just doing what they can with the limitations," Mann said.

Complicating the situation further isAirTran’s hub in Atlanta, which allows it to fill many of its flights with connecting passengers. Southwest, which is more of a point-to-point carrier, eventually plans to dismantle the hub, which will require an entirely different business model once Southwest's transition is complete. .

Mainz said AirTran has "a very large and smooth running operation in Atlanta and that will continue to be important throughout this integration. For the foreseeable future, AirTran will have a significant presence in Atlanta."