That was one of the questions I was wondering about. I recently looked at a new factory in the bay area of prefab houses (
http://www.youtube.com/watch?v=UmpRRoNqsDI)and one of their claims is they can put up a house in 7 days. But of course it isn't that they start with dirt and 7 days later there is a house, there is a time to build the foundation, and the house is built in a factory, but once the foundation is ready and the house manufactured, it only takes 7 days to install and unfold it. Which is still pretty cool.
So one way this headline could be strictly true is if all of the floors of the building were fabricated off site, once they were ready the company might be able to assemble the final building, in a prepared foundation, in 90 days. That is the only interpretation I can think of that works.
Concrete can take 4 weeks to get to 90% strength [1], so if you didn't do the prefab route you would have to spend more than 90 days just waiting for the lower levels to cure so that you could build the upper levels.
I am interested in what they are trying to do though, it sounds like an interesting challenge.
[1] http://en.wikipedia.org/wiki/Concrete#Curing