Do the other intended tracks have an Event in the Event List (meaning they did record audio but there was no signal to record). If so the likely issue is with the setup in the scarlett mixer sending to RB.
Or
Try highlighting just one track to record to. RB should record all selected tracks and put them on the next available tracks; when you try recording this way does RB change those tracks in any way? (ie keep audio or add an Event). You should see RB write those extra tracks when you stop recording and it writes the tracks .. it would be visible momentarily in the popups that occur while writing the recorded data.

These are a couple tests that may narrow things down.
I assume you are using RB and not BiaB, as BiaB does not allow multitrack recording.

I do not work here, but the benefits are still awesome
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