While ago, just for fun, SUCCESSFULLY compiled JNOS-2.0k on Debian-8.7/64 bit with CFLAGS -m64
This binary is running right now on desktop PC instance of JNOS: 2LPJNS:SP2L - simply flawlessly... Hi!
Ok, that is good! I once tried this with NETCHL and it failed, and I did not want to spend the effort of going through all code to make it 64-bit secure, and this is a waste for such a program anyway (it does not require large integers or pointers that can access more than 2GB). So for NETCHL the -m32 flag is mandatory.
Of course, with Debian8.7 there still are several compiler options (4.6 - 4.9 and maybe more) so there may be some issue with a different version of the compiler, I have seen that happen in the past.
Otherwise I have no clue what could be happening, we would need at least the stack backtrace and maybe more.
Rob