What was done to stop the capillary moisture transfer from the concrete floor? Where all these sleepers pressure treated lumber? Was a poly vapor barrier installed first over the concrete? Thinset is what to use, but you do not use it or lay tile over plywood. You need to cover with 1/4" cement backer board first or a isolation membrane like Ditra. Since it sounds like your floor may not have been installed correctly I would strongly recommend the Ditra to provide isolation membrane and a vapor barrier.