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But puppet refuses to read in this change. I know that it automatically and immediately reads in changes to puppet.conf in linux, but is there something that needs to be done to get the windows agents to reflect these changes? Specifying the server name in the command line works, but not in puppet.conf.

To the best of my knowledge, puppet.conf is re-read ever time an agent run begins. It would certainly be re-read when you invoke puppet agent -t on the command line.

Is there any chance Puppet isn't interpreting the configuration file you think it's interpreting? A common gotcha is that Puppet maintains per-user configuration files, and only reads the config file in ProgramData when invoked as an administrator.

An easy way to confirm that Puppet is running with the expected configuration is to invoke the puppet config face. Try puppet config print and check to make sure that config is what you expect it to be.

It's also good to invoke puppet with the --configprint option. Puppet permits you to use a different configuration depending on how it's invoked. E.g. you might get different results from puppet apply --configprint server and puppet agent --configprint server (I'm aware that this is a bit nonsensical in the case of puppet apply...)

Hopefully one of those suggestions will help you debug your problem.