Your mistake was that you said to go though the loop if i was equal to 0, when it wasn't. You want the loop to loop until i is greater or equal to zero.
for(int i = (checkpoints.Count - 1); i >= 0; i--) // your mistake was here
{
if(checkpoints[i].active == 1)
{
playerPositionX = checkpoints[i].xPosition;
playerPositionY = checkpoints[i].yPosition;
camPositionX = checkpoints[i].xPosition;
break;
}
}