Okay, I hadn't tried the join waypoint, i just thought it might be an avenue to check out.
The way I did get it to work, however, was by having two groups of infantry and one of them just got into the CH47 by following the 'get in' waypoint.
The other group also had a 'get in' waypoint, but it didn't work until I put "this AssignAsCargo CH47" in each and every one of those 11 troops' init fields. (ch47 being the name i assigned to the helicopter.)
Good luck. If you need more help, I'll just save you the mission, and you can check it out for yourself.
Anton
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Are you trying to get them to start in the helicopter right away? Because if you are, then you have to use the MoveInCargo command.