i just click on the waypoint to activate it and then move it with the mouse.
No problems here, maybe it helps that i am a newbee with the FMB, i don't know what to expect ;-D
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Win 7/64 Ult.; Phenom II X6 1100T; ASUS Crosshair IV; 16 GB DDR3/1600 Corsair; ASUS EAH6950/2GB; Logitech G940 & the usual suspects

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