This option is called "Record microphone into separate audio track" not the "Record microphone into separate audio file".
Microphone is recroded into the same file but on different audio track. If you put your recording into video editor you will see two separate audio tracks. Also, when watching your recording in Action! Player press A key to change the active audio track.
If you want to record microphone in separate file then go to Settings -> Audio, enable AUX audio feature and select your microphone.
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