Canot set pin as output

"ERROR: FPGA reload not supported"
likely means that you have built your bitfile from older source
(the reload function was added maybe a 1.5 years ago or so)

Did you verify that you have the correct pin by reading the input?

I am building it from master branch of git://git.linuxcnc.org/git/hostmot2-firmware.git. Is there a newer source?

Thank you for your help! I nearly solved the problem. When I was playing with the configuration, I noticed the pin has a correct logic value during Axis start-up and than after half-a-second it goes wrong. The reason for this was that the watchodg time-outed and made all IO pins inputs. If I raise watchdog time-out from 5 to 50 ms, everything works. However it a mystery for me, why it time-outed (it means it skipped more than 5 servo-thread cycles). Do you have any tips, how to debug timing?

did you run a latency test

the latest source is from Mesa (say 5i24.zip)