Concerns have been raised about apparent "anomalies" in BBC journalist Andrew Gilligan's electronic notes of his conversation with Dr David Kelly.
Gilligan's handheld computer is in the spotlight
The Hutton inquiry heard that Mr Gilligan's personal organiser contained two versions of his meeting with the weapons expert and just one mentioned Alastair Campbell.
Appearing before the inquiry into Dr Kelly's death for a third time, the BBC defence correspondent denied writing up his notes some time after they spoke.
Also on Thursday, Ministry of Defence personnel boss Richard Hatfield told the inquiry that, with the benefit of hindsight, he should have suspended Dr Kelly as soon as he admitted to contacts with Mr Gilligan.
It also emerged that Defence Secretary Geoff Hoon had been present at the meeting when the MoD's strategy over naming Dr Kelly was discussed.
Mr Hoon had already told the inquiry that he was "not party to discussions" about the issue.
Dates and times
But the MoD's director of news, Pam Teare, said on Thursday he had been at
the meeting and may already have had a copy of the "question and answer" briefing sheet for press officers fielding journalists' questions about Dr Kelly's identity.
Dr Kelly's apparent suicide came after he was named as the suspected source for Mr Gilligan's story about the government "sexing up" intelligence in its Iraq weapons dossier.
Forensic computer expert Edward Wilding told the inquiry he was worried about why Downing Street media chief Mr Campbell's name did not appear in the first memo on Mr Gilligan's personal organiser.
MoD personnel director Richard Hatfield
MoD director of news Pam Teare
Edward Wilding, director, Data Genetics Ltd
Professor A J Sammes, Centre for Forensic Computing, Cranfield University
BBC defence correspondent Andrew Gilligan
Explaining his findings, Mr Wilding said: "Somebody was looking at creating memos and seeing if dates and times could be changed."
Mr Wilding said there was one memo which was different from the version of notes of Mr Gilligan's Kelly conversation handed to the inquiry.
Mr Gilligan has claimed that Dr Kelly said Mr Campbell was responsible for transforming the weapons dossier in the days before its publication.
Checking with Kelly
Another computer expert, Professor Anthony Sammes, said the best evidence would almost certainly still be in the back-up system on Mr Gilligan's laptop.
The inquiry heard the reporter had been reluctant to grant Prof Sammes access to that machine on grounds of confidentiality.
Asked by his barrister about the experts' findings, Mr Gilligan said he had not carried out any experiments on his organiser before handing it to the BBC on 18 July.
The memo which first mentioned Campbell was a file created at the end of the meeting with Dr Kelly when he was agreeing the quotes he was using for his report, Mr Gilligan said.
It appeared to be on the day after the first memo because the clock was wrong on the organiser and so had changed date during the course of the meeting.
Other changes to the memo reflected the alterations Dr Kelly had requested, he said.
The evidence came after two senior Ministry of Defence officials defended the way Dr Kelly was treated amid tough questioning from the dead scientist's family's lawyer.
Mr Hatfield said the scientist had not appeared to be suffering an unusual amount of stress given the circumstances.
He denied the scientist had not expected to be named as the source.
Teare: Press office has no welfare role
Dr Kelly's name became public just over 24 hours after the MoD put out a press release saying an unnamed official had admitted meeting Mr Gilligan.
To go alongside the release, press officers were told in a "question and answer" sheet to confirm Dr Kelly's name if it was put to them by journalists.
Mr Hatfield was among officials who interviewed Dr Kelly twice about his BBC links.
In his evidence, Mr Hatfield said: "I was very surprised to hear that he thought we... betrayed him because I think we gave him a lot of support."
Under tough questioning from Kelly family QC Jeremy Gompertz, the personnel director stood by his claim that Dr Kelly was given "outstanding" care by the MoD.
Mr Hatfield also said it was a "fundamental failing" for Dr Kelly not to have reported his conversation with Mr Gilligan and he wished he had instituted disciplinary proceedings when the weapons expert had come forward and suspended him.
Later, Mr Gompertz asked Ms Teare why it had taken two hours for the MoD to tell Dr Kelly his name had been confirmed.
Ms Teare said the scientist had already been warned to consider staying with friends because of the amount of media interest in the story.
Top MoD civil servant Sir Kevin Tebbit had authorised the Q&A, which was not used until 9 July, she said.
Ms Teare said she believed she had discussed the Q&A with Mr Hoon and others at a
regular morning briefing on 9 July, before Dr Kelly's name had been published.
"I cannot recall the detail, although it is likely that I would have given a brief outline to the secretary of state," she said.
When Mr Gompertz asked if she had shown the document to Mr Hoon, Ms Teare replied: "He may have had it already, I do not know."
The Hutton inquiry is due to end on 25 September and the findings published some time after October.