"When I get to the end of the course, time just runs out and I have to do the course over again."
You made a mistake somewhere in the course. The instructor doesn't always stop you or warn you immediately. However, he does let you know where you went wrong. Every time you complete an obstacle correctly, you get some sort of praise ("Good Job", "Hooah!", etc.), up until you miss an obstacle, then he stays silent. Run through the course again and notice when he stops giving you feedback -- that's where you messed up. The most common problems are on the fifth obstacle (the second high climb) and straying outside of the white posts. (There are a few spots where you have to jog a bit to one side or the other to stay on course.)
"I'm coming down the fifth obstacle, and the instructor says 'That's not the Army way' before I even reach bottom. I try climbing, jumping, nothing seems to help"
Typically this means that you crossed the obstacle improperly. To cross this obstacle: