Do your Prefs-Audio settings resemble below?
If not what differs?

When it tries to record to 2 MONO channels it also puts each channel (L & R) on its own track.
Then you pan them however you want.
One goes to the assigned track (Left) and the other (Right) goes to the next available blank track. It works that way here anyway..

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InputAssign.jpg (26.78 KB, 24 downloads)

I do not work here, but the benefits are still awesome
Make your sound your own!