1. Create a new project using "File" -> "New File or Project..." -> "Non-Qt Project" -> "Plain C++ Project (Qbs Build)".
2. Go to Projects mode, run configuration and check whether "Run in terminal" is checked.
3. Add further kits to the project and check for these, too, whether "Run in terminal" is checked.
   Usually "Run in terminal" seems to be not checked. In some cases, it is checked, though. Unfortunately I could not figure out yet what makes the difference.

Maybe "Run in terminal" should be checked by default for Plain C++ projects. It definitely should use the same default value for all kits.