Consequently, when John Connolly took over from Jones, Dunning found himself out of the team with Queensland Reds duo Greg Holmes and Rodney Blake handed the chance to impress.
Things went from bad to worse for Dunning when he was suspended from the Waratahs early in the 2006 Super 14 season for on-field fighting.
During his time on the sidelines, Australia Under-21 prop Benn Robinson cemented a starting spot in the New South Wales team and relegated Dunning to the bench for the rest of the season.
Dunning's career suffered a further setback earlier this year when he sustained a knee injury in one of the Waratahs' pre-season games in January and was ruled out of the first five weeks of the 2007 Super 14 season.
But it now appears Dunning's luck has changed.
Not only is he making his return to the Waratahs squad for this weekend's Super 14 game against the Bulls in Sydney, but he is making his comeback at a time when the Wallabies are suffering an injury crisis in the front row.
Holmes (shoulder) and Blake (ankle) will miss the rest of the Super 14 and will be out for most of the Tri-Nations series against the All Blacks and Springboks in June and July, seriously disrupting their preparations for the World Cup in September.
Dunning is keen to make the most of his opportunity.
"It's everything, there is no point lying about it," he told the Daily Telegraph.
"If I want to continue playing in this country I've got to be playing good footy."
Waratahs coach Ewen McKenzie agreed Dunning is in with a real-shot of winning back his spot in the national team.
"Regardless of the injury status in the Australian front-row at the moment, I still thought he was going to be a fair contender in his own right," McKenzie said.
"But he needs to prove that on the field. That is where it really happens.
"Maybe now he can re-adjust the selectors' thinking - you can talk about that but he actually has to make that happen.
"He was in good shape and right there mentally and the injury in the trial was a blow.
"Now it's important that he takes the opportunities he gets and pushes his claims."