When creating a copy of a build-configuration for projects with the Hex Utility enabled, CDT fails to update the <toolChain>/secondaryOutputs attribute to match the ID of the new Hex tool's <outputType>.

Note that for new custom build configurations that were created by copying an existing one with the hex utility enabled, simply disabling the hex utility in the new configuration is not enough. The configuration needs to be manully “repaired” (.cproject manually edited). For any new custom configurations created AFTER the hex utility was disabled in the original configuration, those will be fine.

Hence there two options for existing custom configurations that were copied from an older one where the hex utility was enabled:
1) Delete the existing custom configurations, then disable the hex utility in the original configuration, and then create the new custom configuration again
2) Repair the existing custom configuration

#2 will require the .cproject being sent to TI engineers for analysis and modification.