In the latest Autotools build that works with CDT 4.0.0, when binaries are created by an Autotools project, they are not recognized as such by the CDT and they do not appear in a Binaries folder under the project nor do they have a default run action associated with them (one has to set up a run dialog entry). The problem is traced to the fact that Autotools projects use a separate build directory that is set up as part of the configure tool. The CDT does not recognize changes to the build directory made for the project and is defaulting to the configuration name ("Build (GNU)") when looking for binaries. This has been confirmed by manually creating the folder and copying in an executable binary.
Problem fixed.