How many crosses?
Ideally you'd like for the spokes to be tangent at the hub flanges and radial at the rim. You can't have both so every wheel is a compromise. If you have a hub that has unusually tall flanges, the spoke angle relative to the rim is increased. My bet, without seeing your wheel, is that reducing the number of crosses will solve your spoke breakage problem.
FWIW, I have a personal friend who owned a Bike Friday triple that had an IGH rear wheel. From the beginning it broke spokes at the nipple at an alarming rate. He had the wheel replaced by Bike Friday and later rebuilt by another wheel builder but the spokes kept breaking. He brought it to me and I rebuilt the wheel with fewer crosses. Problem solved!
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