I read throrough the MS Doc and I'm happy that my machines are configured correctly. I do not now believe that domain level authentication is involved in my problems. I am able to fully discover some machines in my infrastructure, I only appear to have problems if they are running ISA server, but even if I disable ISA I still have problems.
This is not an ITA problem, but a raw SNMP one. I am unable to get a successful SNMP Ping from my machines. I think I'll have to get a sniffer out and see if I can't do some lower-level diagnostics. Very irritating.
If you have any suggestions on troubleshooting SNMP I'd be very grateful to hear them, I've never had these problems before and am not well equiped to troubleshoot them at the moment.