OK Finally solved this little riddle. Turns out is was not in the nsclient.ini but in the Nagios config. I've been using Nagios for a really long time and a bit stuck in my ways so I've never sent ARGs over NRPE before now I am and it works great. Who knew? LOL
So for our environment I did:
command_line $USER1$/check_nrpe -H $HOSTADDRESS$ $ARGn$
service_description Check Services
check_command check_nrpe_args!-c check_service -a "exclude=clr_optimization_v4.0.30319_32" "exclude=clr_optimization_v4.0.30319_64"