He had to do it manually because some FD/GPS system was not correctly functioning or was inop, and then after doing this there was no warning that the plane's current position was suddenly registered as several hundred miles away from its last position. (correction, there were some warnings that were noticed but disregarded as they were very short and disappeared momentarily)
On takeoff, the autopilot was engaged and dutifully turned its heading to the course believed to be from the current (erroneous) position to the first desired waypoint -- throwing the plane into an unexpected large turn in a low altitude risky phase of takeoff. The pilots correctly saw some problem, but incorrectly then carried out a series of mistaken recovery steps leading to full disengagement of the plane's normal coordinated flight controls ("normal law", etc) to try and get it to behave. Apparently, everything except just shutting A/P off.
Well, one thing cascaded on another, the plane couldn't be reset back into normal flight control mode, there was fog, etc. and they couldn't land back in MEL and had to divert several hundred miles to SYD or wherever and a whole incident. It could have been even worse.
Seems that complicated systems... can get complicated easily if you overlook or start off unsure of what has gone wrong.