As others have mentioned, the required fix is adding stty -ixon to your ~/.bashrc file. However, it should be protected from execution by non-interactive shells:
if tty[[ -st &&0 echo&& "$$-" | grep= -q*i* i]]
then
stty -ixon
fi
This should avoid errors when there is no TTY or interactive session in the first place, so "internal" shell invocations of desktop environments etc. will not cause error messages.