Probably intentional on PG Music's part, and let's be clear, Band in A Box does an absolutely fantastic job of handling the complexities of music scoring. There's little question about that.

But in pure form, if a song has a flat (or sharp) in its key signature, and one of those notes affected by the key signature needs to be played as a natural (or sharpened or flattened), then the correct notation is to show the adjacent note with an accidental to force the natural to be played, or to use a double-flat or double sharp to achieve the same.

Here's an example (from Beethoven, Opus 27 2nd movement). Note the C Flat values to achieve B natural as opposed to just placing a natural in front of the B flat.

(Anyway, great work PG for what scoring features we have already received...)

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