See here for details on the configuration files location:
http://www.visualbuild.com/Manual/co...ationfiles.htm
VBP only updates the .config file on exit if changes were made to the configuration, so you might avoid making changes to the config from the build. Another possibility would be to add a Wait step (to wait a few seconds) after the step that launches the secondary .bld file so that if the first instance does update the config file on exit, it will do so after the second instance has already read the file.