I suspect there is a direction arrow that you aren't seeing, as it might be hidden in the part. When you created the Setup, did you specify that body, or is it seeing another one in the setup?
If neither of these lead to a solution, could you share the part here? As it's not an assembly of linked components, File > Export > Save to local folder. Return to thread and attach your .f3d in your reply
I highly recommend not counting on the face selection to give you want consistently. Your best bet IMO is to select open contours for the geometry (think of this as the machining boundary) and then select the appropriate Stock Contours (sometimes isn't needed with appropriate contour geometry). Keep in mind that when you select faces the software is making its best guess in a "dumb" toolpath that is not model-aware. Sometimes this is affected by how the part is modeled even.
Edited to add an example:
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