Hi Nick,
well, there's an important difference between entering a move sequence or entering the resulting position, and this difference is castling rights!

Among all the hundreds engines in MessChess I only remember 1 or 2 which allow entering castling rights when entering a position, and so this option is not implemented in any plugin (for WinBoard or Arena).
IOW, from your FEN string (in WinBoard) only the following part is used in the plugin (and entered in the engine):
r1bq1b1r/ppp2kpp/2n5/3np3/2B5/8/PPPP1PPP/RNBQK2R w

So it's just the engine's decision, whether it accepts (or makes itself) any castling moves depending on the positions of the king and rooks.

Regards,
Franz

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