I loaded a position in the setup part of the analysis and it said it was a custom position:
But when I loaded it again with the Load FEN option, it said it was a Chess960 position:
That's not a bug.
What do you mean? It's not a Chess960 position.
I believe all custom positions, that don't start from the standard opening position show up that way under an Analysis Board. So, not a bug but a design decision.
Oh, okay.
I loaded a position in the setup part of the analysis and it said it was a custom position:
But when I loaded it again with the Load FEN option, it said it was a Chess960 position: