Thanks for your replies guys.
Nigel, I don't have any trouble with the transport unload WP either in singleplayer, however when I try this online the chopper just hovers over the WP, forcing everyone to use the eject function instead.
Disabling the AI's auto targeting is a good tip, didn't think of that one.
Terox, there is no AI in the helicopter with the exception of the pilot and the gunner (or do these also cause this bug to appear?). I tried this online with one other human player, the helicopter just hovers over the WP. Also I've been looking for a script to handle this problem but I can't seem to find any that solve this one.