I asked these questions, too. I have been assured that it is. An LTC2937 is used to sequence power. Power stability is critical to the application (communications DSP) and great care was taken to follow the power-up rules for the Arria and other devices.
At this time there is only the one board. The Arria's other logic behaves correctly; it is only when the LPDDR3 EMIF interface is released from reset (.global_reset_n) that the huge power draw occurs.
Following the release of reset, no activity is observed on the differential clock (or any other line) going to the Micron LPDDR3 ram. The testing engineer reports that the CKp line out to the RAM (B13 on the Arria U19) is pulled up to 1.2V before Arria configuration. Afterwards it floats with little or no drive current.
A Questa simulation of the full calibration process, using a Micron model for the RAM, succeeds in "calibration" in roughly 3.5mS sim time. Yet we see nothing of the sort in the real world.
We find all of this very surprising as our group has been using Altera (now Intel) parts since the last century and have never run across a difficulty of this sort. They usually just work. This is, of course, a critical problem for our project.