Can VREF be other than VCCIO/2?

I am sure those resistors are 1K. I've also tried 100ohms, but just to see if it changes something.

Thats my own PCB with EP3C40. Two boards are behaving the same, so I suppose the problem could be somewhere in the schematic. I've connected all VREF pins to 1.25V and all banks where memory is connected is powered 2.5V. The FPGA gets hot only when I upload a design which use memory controller. The PLLs are fine - separately works OK and using altmemddr works fine too.

Series termination: 22ohm, parallel termination 47ohm. I am not sure where else I could do a mistake.