I just had the same problem fixed with mine. It started in first, then moved on to third, and got really bad.

It was the bearings in the transmission on the shafts that the gears are on. It was allowing them to slide with the clutch was let out, knocking it out of gear in gears at the top of the pattern.

One way to check would be to have him drive and shift into second and hold the shifter. When he lets the clutch out see if the shifter moves forward in his hand.

It wasn't too expensive to fix. We took it to a mechanic who knows toyotas and he said it was common. He just had the truck one day.