According to Variety there has been a tussle for power between Legendary's Lin and Roy Lee and Warner Bros. (who will be distributing the movie worldwide apart from Japan which will be dealt with by Toho) as they have differing ideals on how the film should be - which could explain the most recent change to the script.
Back when the film was announced in 2011, David Callaham (The Expendables) wrote the first draft which was then re-written by David S. Goyer (Batman Begins) before being re-written again by Max Borenstein (The Seventh Son) before landing in the hands of Drew Pearce (Iron Man 3). Now it seems that Frank Darabont (The Mist) has taken on the task to re-write the relaunch for The King of the Monsters. Signing on as the fifth writer for the project, Darabont now has a short amount of time to turn the script around before the film heads into production.
Another point of contention between Warner and Legendary comes down to casting choices. Warner (as you can well imagine) wants a big name star to headline the movie to draw in audiences. According to several sources, Warner are interested in Henry Cavill (Man of Steel) and Joseph Gordon-Levitt (Looper) for the lead role. However the JGL rumour has already been debunked with new reports that he may be joining the cast of Sin City: A Dame to Kill For. Legendary on the other hand are looking to cast either Scoot McNairy (Monsters) or Caleb Landry Jones (Contraband) for the lead role of Gareth Edwards' (Monsters) reboot.
All of this has led to plenty of tension between Warner and Legendary. As per Variety's report, this has led to Dan Lin and Roy Lee being ousted from the Godzilla project and replaced by Mary Parent, the producer on Legendary's other kaiju endeavour Pacific Rim.
With all of the script changes and no casting choices being made, it should come as no surprise that there has been a lot of problems behind the scenes of Godzilla's return to the big screen after a 10 year hiatus (or 15 if you're going by American versions). However with Godzilla scheduled to be going into production on March 14th in Hawaii, there's just over two months for Darabont to get the script re-write finished and for Warner and Legendary to agree on casting to hit their 2014 release date (and Godzilla's 60th birthday).