The "setboard" command doesn't seem to be working in 6.0.3. If I run the following, the engine never comes back with a move:
printf "xboard\nprotover 2\nsetboard r3k2r/pp2bppp/8/3p4/3n4/3NR3/PP1P1PbP/2BK4 b kq - 0 1\nst 1\ngo\n" | ./gnuchess
I noticed that on the other hand, "epdload" seems to be working fine. From what I can tell, the difference is that cmd_setboard isn't calling SetDataToEngine. I added the call to cmd_setboard (patch included) and it fixed the issue for me.