TFS 2008: Team Build doesn't get subfolders of team build type folder by default
In TFS 2005 subfolders of your team build type folder were copied recursively to the build temp directory. In TFS 2008 only the contents w/o recursion is copied.
To change this behavior, Aaron tells us, you need to modify the following line
<add key="ConfigurationFolderRecursionType" value="Full" />
in the TfsBuildService.exe.config on your build machine.
Enjoy!