Shanks (27) was defending her world title in Denmark but slipped out of the gold-medal reckoning when she finished third in the qualifying heat behind American Sarah Hammer, who topped the qualifying times with 3min 27.826sec.
Hammer later beat Great Britain's Wendy Houvenaghel in 3min 28.601sec in the gold-medal ride.
Shanks lost her ride-off for bronze when she was pipped by Lithuanian Vilija Sereikaite. Shanks had posted a time of 3min 31.259sec to finish third in qualifying then recorded 3min 32.733sec against Sereikaite.
Shanks told TVNZ her "training had gone really well leading in and I was really looking forward to the race. But it did not quite come together today.
"As long as I can learn from it and move forward then I think it can only be a good thing for my overall career."
Shanks was involved in prolonged drug testing after her race and was not available to talk to the Otago Daily Times.
Shanks and her coaching team were left scratching their heads after she failed to kick on in the final kilometre of both her qualifying ride and the ride-off for a bronze medal.
Her coach, Craig Palmer, was naturally disappointed at the unexpected result.
"It is difficult to put my finger on it," Palmer told the Otago Daily Times from Copenhagen.
"It was a disappointing ride in the first round when she didn't reach the standard needed to go for the gold medal."
Palmer remained puzzled because Shanks was in good form leading into the championships.
Her training had pointed to a sub-3min 30sec ride and Shanks was shattered she could not deliver.
"But it didn't happen on the day and we will have to delve into the reasons for it before Ali starts training for the Commonwealth Games," Palmer said.
"A number of things need to come together on the day. Her time in the first round was just 0.3sec slower than the time Ali rode when qualifying at the world championships in Poland last year."
Shanks had little time to dwell on her disappointment as she prepared for this morning's team pursuit qualifying.
Shanks seemed to be on schedule for a sub-3min 30sec ride in the qualifying round after unleashing a 1min 07.976sec second kilometre, but she was not able to push on in the final 1000m.
She was 1.8sec behind after the opening 1000m in the ride-off but had closed the gap to just 0.1sec before the final 750m. Again, she failed to lift her performance.
"Ali didn't back up well on the second ride and that is unusual," Palmer said.
Palmer knew Shanks would not be able to keep up with Sereikaite in the first kilometre because the Lithuanian is the fastest starter in the world. But she was expected to collect the bronze medal when she had reduced the gap to just 0.1sec with 750m left.
Her failure to kick on surprised all the coaching staff.
"She didn't keep rolling and go over the top of the Lithuanian," BikeNZ high performance director Mark Elliott told the Otago Daily Times from Copenhagen.
Elliott expected Shanks to be on the podium.
"Every rider we send to the world championships has the chance of winning a medal," he said.
"Ali is a good athlete and I'm sure she will come back and medal at the Commonwealth Games in India and come back strongly for the world championships next year."
Shanks' team-mate, Hamilton's Jaime Nielsen, produced a creditable 3min 37.212sec to finish seventh in her first ride at a world championships.
The emerging trio of Adam Stewart (23), of Christchurch, Sam Webster (19), of Auckland, and Eddie Dawkins (20), of Invercargill, were a meritorious fifth in their debut in the men's team sprint.
They produced a strong ride to clock 44.450sec for the three laps, the fastest by a New Zealand team and good enough to beat the sprint superpowers of Russia, Australia and the Netherlands.
Their time was 0.2sec faster than their New Zealand record set in Invercargill last month, and only 0.6sec off Olympic champion Great Britain, which missed out on the gold-medal ride behind France and Germany.
Elliott said the sprint team was expected to finish eighth, so the fifth place was a bonus.
"They were just 0.3sec short of qualifying for the medal round," Elliott said.
"We are excited about their prospects because they are still effectively boys.
"They are just two years away from gaining men's strength and it will be good as we lead to the Olympics in 2012."
