With a C++ file up, go to Tools -> Beautify -> Edit Current Profile, and in the dialog that pops up, go to Indent -> General, and make sure "Indent with tabs" is on. That's the setting used when editing code, or when a section of code gets reformatted due to alias expansion, etc...
If that is turned on, then go ahead and post your user.cfg.xml file from your configuration directory. There are some features like Adaptive Formatting, and configuration file support that can override that setting, but getting the config file is probably faster than sending you to several places in the config dialogs.