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OK, I see what causes the problem. Indeed there is a bug in Joker's FEN
reader. If there is a King in the initial position (f1/f8), it also sets
the flags for Rooks being in the initial position.

Normally this bug should not be tested at all, as WinBoard is not supposed
to pass incorrect FENs to the engine. Indeed, the version of WinBoard that
is on my website now, (awaiting its official release as WinBoard 4.3.14,
any day now), does not, and simply strips off the kq castling indicators
as it sees there are no black Rooks on a8/j8. It just seems that the
version of WinBoard that I used here was less strict in this area as
well.

Anyway, I will fix the bug next time I will do some work on Joker80. (I
want to equip it for FRC/CRC, and this requires an overhaul of the
castling code everywhere.) In the mean time, you could already download

http://home.hccnet.nl/h.g.muller/alpha.tst

and replace your current winboard.exe by it. Then illegal FENs with
illegal castling rights would be corrected by WinBoard and corrected
before they are passed to the engine.