No mystery there.
But Kaepernick came clean to the Sacramento Bee Tuesday in disclosing the severity of the injury, saying he had a "chipped bone on his forefoot and a ruptured capsule in the ball of his foot" suffered in a Week 2 loss at the Seattle Seahawks.
And after rushing for 87 yards on nine carries in that game, Kaepernick did not surpass 20 yards rushing in a game for another five weeks.
He still rushed for 524 yards on the season, second among 49ers quarterbacks in franchise history to Steve Young, who ran for 537 yards in 1992.
Now, Kaepernick insists it's all in the past. Especially since he did not have to undergo surgery on the foot in the offseason.
"Just rest," he said of his recovery.
"It's a non-factor. It's a year-old injury now."
Kaepernick has only appeared in three series in two exhibitions thus far, and has not attempted a carry.
The 49ers have yet to score a touchdown in the preseason and have been outscored by a combined 57-3. So what do they need to do offensively, keeping in mind the starters have not played all that much?
"Just establish a rhythm," Kaepernick said. "I think that's the biggest thing we need to get right now."
And with the third preseason game this weekend against the San Diego Chargers at Levi's Stadium -- traditionally, that is the exhibition teams utilize as a dry run for the regular season -- you would think the 49ers would play their starters the most to establish said rhythm.
"Yeah, we're going to try and get in a rhythm in every game that we play," Kaepernick said. "How much we play is going to be determined by coach."
Coach Jim Harbaugh was asked if Kaepernick would play more against the Chargers.
His answer? "Maybe."