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My first reaction is that something must have gone wrong installing the new
WinBoard alpha, and that you are somehow still using an old one. When I
start the alpha with this FEN with two Joker80 engines, I can see in the
debug file that the FEN really sent to the engine only has KQ, not KQkq
castling rights.

So first check: click the 'help -> about' menu item on the WinBoard that
you are using, and check if it says WinBoard 4.3.14k. If not, we have a
mixup.

If this is indeed WinBoard 4.3.14, it is not possible for me to make any
sensible guess as to what is wrong without having the winboard.debug file
of this game. (This file records all communications between engine and
WinBoard.) WinBoard should be started up with the option /debug on the
command line to instruct it to make this file. (And when an irregularity
happens, immediately rescue that file by renaming it, before you restart
WinBoard!)

If Joker80 would castle when receiving a FEN that says it has no castling
rights, it is inconceivable that H would not have noticed that before, as
I played many thousands of games with it, also from positions without
Rooks (but then I also deleted the castling rights for that side, as
WinBoard 4.3.14 does here in my tests too). As you can see, WinBoard does
not accept such a castling as a legal move when it is actually done, not
even the version that erroneously passed the non-exsting castling rights
to the engine. And even though I don't examine every game I play, I
always scan the PGN file of a large run with a text editor for the
occurrence of the string 'forfeit' and 'on time', to see if there were
problems.