I have spent numerous hours trying to publish the UDDI services in the ESB Toolkit using UDDIPublisher.exe. I have received pretty much every error possible, from 404 to 503 to the entire IIS falling apart. I just found the solution: don't install UDDI as a normal Windows 2008 role, but install UDDI3 as a part of the BizTalk Server install.
At one point I managed to get UDDIPublisher.exe to install the services properly, but I cannot remember the route I went. Most likely it included changing permissions in IIS, UDDIPublisher.config as well as ApplicationHost.config and also fiddling with the account used to run the whole shebang. By installing UDDI from the BizTalk DVD and then running the publishing exe, it works without a hitch.