The Brit crashed in the one-lap time trial on the opening day, forcing him to sit out the first Madison event on Tuesday.
His back wheel appeared to slide out and Cavendish said ahead of his victory on Wednesday that it was down to a new bike position he was experimenting with.
"I'm a bit banged up after yesterday [Monday], obviously, but I feel OK thank you," the 34-year-old told Belgian outlet Sporza.be.
"It's a complicated story, but basically my position's changed; my weight's a lot more forward, and actually I hadn't done any test runs on a flying lap, and my weight was just too far on the front, and I just couldn't turn the bike.
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"Going around the banking, I knew half a second before that I was f*****, really. I was still above the red [line], and I knew I was going down. It's a tight banking, you know? It's a real tight track; you really have to steer the bike, and I couldn't steer back.
"I knew I was going to come down, so I could prepare for it, so I've come off a bit better. But it's not ideal, that's for sure."
Cavendish and his riding partner Iljo Keisse, who won the Ghent Six together in 2014, sit sixth overall out of 14 teams on 58 points, one lap down on German leaders Roger Kluge and Theo Reinhardt.