There are 2 ways to add a new build configuration:
Through the Eclipse CDT wizard (Manage Build Configurations dialog, Add button…) with many options and traps…
Through the New Open AT Configuration wizard provided by DS, which is the recommended way (project right-click menu > New > Open AT Configuration)
The symptoms you have sound like issues related to “badly” created configuration through CDT wizard.
Could you give a try with New Open AT Configuration wizard?