Yes you are right in inferring that I meant CCS. The TI ARM Compiler Tool version is 5.1.1
I appreciate the prompt responses.
Initially I had left the Manage the target configuration automatically check box in checked (default) state. That was giving me a lot of problems in that it was making the GUI build configuration options ineffective and only invoking the options in the mk files. It was also running a whole bunch of tasks when compiling a file.
Once I unchecked that, things are happening in a more predictable state.