It's really important to ensure that the engine plays near it's best at the start of a chess960 game because without a book database to refer to, almost all engines will play very poorly if they are constrained by skill level. Often their opening choices don't seem natural even by the standards of a amateur.
The modified Stockfish engine works in all the main chess applications and can be downloaded here in conjunction with Winboard-960:
http://www.stockfishchess.com/
Stockfish, a UCI chess playing engine derived from Glaurung 2.1
Copyright (C) 2004-2008 Tord Romstad (Glaurung author)
Copyright (C) 2008-2012 Marco Costalba, Joona Kiiski, Tord Romstad
GNU GENERAL PUBLIC LICENSE
Enjoy 960
Stockfish, a UCI chess playing engine derived from Glaurung 2.1
Copyright (C) 2004-2008 Tord Romstad (Glaurung author)
Copyright (C) 2008-2012 Marco Costalba, Joona Kiiski, Tord Romstad
GNU GENERAL PUBLIC LICENSE
Enjoy 960