Snow Leopard now uses mDNSResponder to resolve DNS.  This behaves differently than older versions of Mac OS X, which use Directory Services for DNS resolution.

One key difference is mDNSResponder doesn’t necessarily start “at the top” of the list of DNS server entries (either added in the Network system preference pane or provided by a DHCP server).  If the primary DNS server doesn’t respond immediately, mDNSResponder tries the second DNS server.  If the second DNS server answers, mDNSResponder may essentially blacklist the first one and keep using the second one until mDNSResponder is reset.

mDNSResponder can be reset by rebooting, or entering this into the Terminal:

sudo killall mDNSResponder

As with the DNS reverse order bug, this behavior can cause unexpected results, especially if you have a DHCP server that is providing one more internal DNS servers, in addition to an external DNS server for a fallback.