Two days of frustration, it seems that Vivado 2015.2 has an BUG related to PS presets and Board Part flow, as soon the system has been configured with LPDDR2 then the board files and presets become invalid. So we have fail a WebCase by Xilinx for this.

It is not a shows stopper, it is possible to provide the presets and board files with LPDDR2 not enabled, and then later apply the required setting per hand.