I have finally been able to book after 10 days and a few emails to/from Emirates.

For those that are trying to look at prices/availability the 'search by price flexible dates' didn't work on our route KL-MLA (except for one week in the year!) , and initially the schedule search always bumped you to business class for the return leg. Then that was solved, but the price was still higher that that given for the same ticket quoted in the available week in the 'price search'

Again that has been solved and the prices are aligned, albeit +$60 compared to before the website upgrade. I believe you should need to know the ball park figure for the fare before you commit.