Stratix V GX kit - flash programming problem: "No Nios II processors available"

We have two boards, one is completely good, one is half-good (this one).

I measured some voltages, but I'm not sure that all of them. It looks ok:

C111, 12V_mux, measured=12.03V

C83, DC_IN, measured=19.03V

C171, "0.9V", measured=0.91V

C236, 2.5V S5_VCCIO_HSMB, measured=2.50V

C116, S5_VCCINT, measured=0.90V

C341, S5_VCCA_PLL_2.5V, measured=2.46V

C505, S5_VCCR_GXB, 0V ???

C525, QSFP_VCC, measured=3.32V

C515, 5.37V_MONITOR, measured=5.39V

C149, DDR3 VTT, VREF 1.5V, measured=1.50V

C286, VREF_HSMB, measured=2.48V

C42, VTT_QDRII_RLD 0.9V, measured=0.89V

C55, S5_VCCIO_1.8V, measured=1.81V

Are any handy test points for this? I did it by randomly picking capacitors and searching through the scheme for voltage on them.

By the way, "LCD is dark" means that there are no symbols on it. Actually it shows filled black line:

And several times yesterday there was another result: "Not connected" on the display:

I do not know what it means, but the working board shows "Connecting..." on the LCD. The behavior depends on power on/offs - sometimes LCD shows "Not connected", sometimes black line. I just do on/off every several minutes and result can be different.

For me, it looks like something wrong with FPGA or memory, it works unstable. And even if LCD shows "Not connected" I can't update flash by Nios II EDS, it tells "There are no Nios II processors available...".