I was having the same issues and someone posted the solution, found at filesystem-api-not-working-in-chrome-v27-v29
navigator.webkitPersistentStorage.requestQuota(1024*1024,
function(gB){
window.requestFileSystem(PERSISTENT, gB, onInitFs, errorHandler);
}, function(e){
console.log('Error', e);
})
You have to remove the PERSISTENT
from navigator.webkitPersistentStorage.requestQuota(...)