The lanky Belgian threw in the towel on the first climb of Stage 1 on Mesa Grande Road after nursing a flare-up of an old knee injury in the week leading up to the event.
Rolf Aldag, who is acting as a technical liaison between the riders and equipment sponsors, is making sure there is no link between the injuries of Vandenbergh, Zdenek Stybar and Tom Boonen - all of whom has had knee pain in the past month.
Stybar underwent surgery at the beginning of May for his injury, and is off the bike for three weeks. Boonen's problems were caused by a series of crashes, the worst of which came in the Tour of Flanders, when he ran into a street sign.
"Even though Boonen's problems were clearly caused by the crash, and Vandenbergh has had surgery on that same knee in the past, we are checking everything about their set-ups just to be sure," Aldag told Cyclingnews. "Even so we will check the insoles, the shoes, the cleats - everything about the set up."
Vandenbergh's problems may have been exacerbated by the hundreds of kilometers he spent in breakaways during the Classics season. The 29-year-old scored the team's top results of the Classics, taking second in Omloop Het Nieuwsblad. He will now focus on getting his knee back to normal rather than jeopardize the remainder of the season trying to battle through the Tour of California.
"We tried everything to get his knee better for this race," Aldag said. "We even brought in Dr. Eric Heiden - he's very renowned here - but he didn't want to force it."
The injuries have been a blow to a team which, on paper, should have dominated the one-day races this year. Instead, their 24 wins to date have all come in stage races.
"It's been a rough ride for the team so far. You could really see the strength of the team in the Classics, but it's hard to replace one of only a handful of riders who can win a Classic. If you take Fabian Cancellara out of RadioShack, they have a much harder time."
One bit of bad luck really grates on Aldag, and that was the moment Stybar clipped a spectator and lost his place in the winning breakaway.
"My main problem with Roubaix is we will never know if he could have won. If he had made it to the line and gotten beaten in the sprint, we could say OK, he was there. But now we just won't know."
The team will still soldier on in trying for a stage win in California. Gianni Meersman was close in the sprint on stage 1 in Escondido in fourth, second in the field behind Sagan, and Sylvain Chavanel is targeting the time trial in San Jose.