This came up locally back in March, when our local website, Felixstowe News, reported on it.
It's essentially due to the fact that when the first part of Felixstowe's original South Reconfiguration plan was made, they didn't think ships would get so big so quickly!
The local council has given it the nod, really, as they say it is part of the second phase which already has planning permission - but they say it isn't enough of the whole plan to trigger Felixstowe's other obligations, like dualling the rail track, etc . . .
Personally, I think that combined with the other developments at London Gateway, etc, it probably means that Felixstowe will put back still further its plans for completing the south development, and the HPUK will effectively dump its plans for Harwich Bathside.
PS: Alan, can't find any docs relevant to the story on the MMO site - do you have a direct link?