The wheelchair racer from Sherbrooke, Que., lacked finishing speed in the 5,000 metres at the Paralympic Games.
Roy initially won gold in the distance in Beijing. She stood on the podium, accepted her medal and heard O Canada.
But the International Paralympic Committee later ordered a re-race. Other countries had protested the result because of a chaotic crash that occurred behind Roy and also because an official ran onto the track during the race to help fallen racers.
The IPC acknowledged it was a mistake to let the medal ceremony go ahead prior to resolution of the protests.
Nevertheless, Roy was forced to give her gold medal back the day before the re-race. She then finished a painfully close second to Amanda McGrory of the U.S.
Her disappointment was of a different kind Sunday. The 41-year-old finished ninth. Roy will race four other events in London, including Monday's 400 metres.
She considers the 5,000 metres her premiere event, however, and best chance for gold.
"Usually I'm racing very well in the 5,000," she said. "Usually my top speed is really, really better than that.
"Maybe it's a bad day. I don't know. I really don't know."
In addition to her silver in 2008, Roy has won four Paralympic bronze medals during her career. She raced in the shadow of Canadian teammate Chantal Petitclerc in Beijing, where Petitclerc won five gold medals and beat bronze medallist Roy in both the 400 and 800.
Roy races in the T54 classification, which is a wheelchair racer with normal arm power and partial to normal trunk movement. She became a paraplegic at age 17 because of a fall from an all-terrain vehicle.
Sunday's race pace was slow as Roy and her competitors saved their breath for a final sprint. Roy was mid-pack for much of the race, but she felt her position for the stretch run was good because she was tucked in behind Beijing bronze medallist Shelly Woods of Britain.
Neither McGrory, Roy nor Woods made it into the top six though. Switzerland's Edith Wolf, Shirley Reilly of the U.S. and Christie Dawes of Australia took gold, silver and bronze respectively.
Roy was baffled that her highest gear seemed to have left her between the warm-up track and Olympic Stadium.
"It was just so slow, you just have to have a good sprint at the end and you're fine," Roy said. "I think everybody is surprised about the top three. Nobody from Beijing is on the podium.
"I think I just need to . . . pfffft, I don't know. We'll see tomorrow."
Saskatoon's Keira-Lyn Frie fared better than Roy with a fourth-place finish Sunday.
"I literally started racing the 5,000 this past January," the 25-year-old said. "That's the eighth one I've ever done.
"I just didn't have that last 50 metres to edge out the Australian (for bronze), but I'm still just on top of the world right now."
Roy will also race the 800 and 1,500 metres as well as the women's marathon on the final day of competition Sept. 9.