Using server variables in a config file

We have multiple servers in both our test environment and our production environment. For the most part our web.config file is the same for each server in a given environment. We have one setting that differs and for those I have am using a server level variable to define the value to put in the config file on deploy. This works great when using the normal deploy process. What I have noticed is that if instead of deploying it along with a package you do a manual deploy of a web.config change directly to a given server that it doesn't apply any of the server level variables. Is the only way to get that to work is create a different instance of the config file for each server? If there are other options what are they? Or perhaps is this a bug?

Product: BuildMaster
Version: 5.5.3

This appears to be a bug - it should work exactly as you have stated. Our internal issue ID for this is BM-2281 and should be released in the next maintenance (or minor) version (whichever comes first).