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I posted the updated WinBoard/Fairy-Max package at
http://hgm.nubati.net/Spartan.zip . 
I also included the WinBoard help file, this time. (But don't look there for info on Fairy-Max; WinBoard is an independent project, and Fairy-Max is just one of the many hundreds of engines that can run under its control.)

This version of Spartan Chess is configured for having black promote to
R+N, and white to Q. (I had to fix a lot of bugs in WB to get that working:
it was not prepared for white and black playing with different piece sets
at all.) The explanation on the encoding in fmax.ini is fully updated. (And
with this version of Fairy-Max, the order of the piece defintions is more
important than it was before, but also this is explained.)

In the mean time, the test with the B+N replaced by B+K has reached 100
games, and white was leading by 54%. Now this is close to the normal white
advantage (which is 53-54%). So after this test is done (i.e. 400 games), 
I will try it with a start position where black has the first move.