WASHINGTON – The software bugs that have plagued the F-35 program for months are largely resolved and no longer pose a threat to the Air Force's goal of declaring its jets operational this year, according to the program chief.

The problem lies with the next increment of software, Block 3i, which the Air Force requires to declare initial operational capability. For F-35s using the original 3i software, the jets' systems would shut down about once every three or four hours and have to be rebooted. This "choking" effect is caused in essence by a timing misalignment of the software of the plane's sensors and the software of its main computers.

The joint program office and F-35 manufacturer Lockheed Martin identified the root cause, incorporated a fix, and have nearly finished flight tests of an updated software load, JPO chief Lt. Gen. Christopher Bogdan told reporters on Tuesday.

The team has flown 44 flights and 96 hours with the new software, and is now seeing a huge improvement in stability Bogdan said after an April 26 hearing of the Senate Armed Services Committee. The jets can fly for about 15 hours between shutdown events, he said, which is more than the eight to ten hours of stability the program office deemed "good enough."

All of the testing of the improved 3i software will be finished by the end of the week, Bogdan said.

"I'll make a decision at the end of this week whether that version of 3i software is it, I'm leaning towards it being it," Bogdan said. "That's going to be the version of software that the Air Force declares IOC with."

The JPO will eventually retrofit all of the existing jets with the new, updated software, Bogdan said. The team will also incorporate the 3i fixes into the next increment of software planned for the F-35, called Block 3F.

Bogdan credited the improvement to "really smart guys at Lockheed Martin and Northrop Grumman and BAE Systems, who own the sensors and stuff, getting down into the nitty gritty and doing good root cause analysis."

Although the problems with 3i are now largely resolved, the testing took longer than expected and delayed the final increment of software by about four months, according to Bogdan's written testimony. Block 3F, which gives the F-35 fleet full combat capability, is now scheduled to be delivered in the late fall of 2017.

While software stability while the jets are airborne is vastly improved, operators are still having trouble booting up the main computer while on the ground. Bogdan has sent a "red team" to investigate the root cause of the problem, and anticipates an answer in the next month or two.

"We are still investigating why on the ground sometimes, starting from a cold airplane, it takes you two, or three times to try and get the computer booted up," Bogdan said. "But right now the warfighter tells us we can handle, that that's not a big deal we know how to deal with that."

Bogdan's decision by the end of the week on whether to move forward with the latest version of Block 3i for Air Force IOC should come just in time to meet the service's target of August 1, 2016, to declare the jets operational.

But one last hurdle remains to Air Force IOC. Work on the latest version of the F-35's Autonomic Logistics Information System (ALIS), the high-tech brains of the plane, could delay IOC by about 60 days, Bogdan told the Senate Armed Services Committee.

Committee Chairman Sen. John McCain, R-Ariz., a longtime F-35 critic, slammed the program during the hearing as a "scandal" that has seen "disgraceful" cost overruns over the years. But in a sign that the program may be starting to turn around, even McCain had some positive words for the witnesses.

"We are making progress," McCain said. "We have challenges that lie ahead, but there has been some significant improvements as opposed to some years ago."

Twitter: @laraseligman