Do you use the latest version of System Workbench ? Please verify it by selecting : Help > Check for updates...
Then delete every debug configuration previously created and associated to your project : Project properties > Run/Debug Settings, select all, then delete them.
Finally, try to recreate the Debug Configuration :
Right click on the project, then choose Debug As > Ac6 STM32 C/C++ Application. It should automatically create the debug configuration and launch de debug.
System Workbench should ask you to create a custom board as Vetch said.
Hope it works,