The Autotools plug-in after successfully configuring and building the first time will on subsequent attempts run the config.status which rebuilds the Makefile. This is done even if the Makefile already exists. When the build console preferences are set to clear, this ends up clearing the original configuration. Suggestion is to only run config.status if the Makefile is missing and the config.status exists.
Fixed in next release. Code has been changed to only run config.status if the top-level Makefile can't be found.