Alex and d lim, thank you for answers) FPGA heats up regardless of project and even in moment his configuration. Removed a number of capacitors on feeds 1.2 and 3.3 not help. Watched thermal imager warming up, hoping to determine the area of the short circuit. The heating starts from the FPGA core and diverges in different directions, while the remaining capacitors on the power supply remain cold. As for the resistance measurements, I will correct the values, since I initially made a mistake. In the normal case, in the off state, the resistance between 1.2 and 3.3 is 500 Ohms. Between 1.2 and GND about 125 Ohms, and 3.3 and GND about 150 Ohms. In the case of overheating, in the off state, between 1.2 and 3.3-11 Ohms, between 1.2 and GND about 5 Ohms and between 3.3 and GND about 6 Ohms. Initially, the second Board also worked fine, but it was debugging other chips and there were many other tests. On malfunction drew attention only then, when observed, that nutrition 3.3 with regulator through coil inductance in 330 MGN has fallen until 2.9 Volts.
Many times the Board was shortened and burned different chips, but each time it was possible to restore its performance. It seems to me that in FPGA something burned down as a result there was a short circuit on internal feeding buses. It is difficult to replace it, so it remains to work with it in this mode. If we can still determine the cause, I will report it. Thanks)