I've finally figured out that my unusual DNS problem with my Mac is being caused by Bonjour adding a local route on 169.254.0.0/16 - diagnosed by it also doing it on a Windows box when installed.
However, I can't find a way to disable it. I never use, I'm never likely to use it - and I don't find having to run "route delete 169.254.0.0/16" as super user ever time I reconnect to the network (such as waking from sleep mode) extremely counter intuitive and not the Mac way.
Is the way to turn off the damn thing, or am I stuck with screwing with routing tables forever more, like 1994 on my Indy all repeating itself...