It's not a waypoint problem, its a heli problem. I'm not an expert - I just stay away from them - but make sure you have had a good look through the chopper tutes in the Ed Depot. Search the forum and the FAQ as well, heli problems come up all the time.
However, to get a chopper to hand in a specific place, its generally advisable to place an invisible H and use put
chopper1 land "land"
in the on activation field of the waypoint that is placed over the H. That should help. Make sure the landing place is flat.