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I've tried actually using the LVDS bank and it turns out we swapped the pair polarity again.
From nMigen comments:
# On iCE40, a differential input is placed by only instantiating an SB_IO primitive for
# the pin with z=0, which is the non-inverting pin. The pinout unfortunately differs
# between LP/HX and UP series:
# * for LP/HX, z=0 is DPxxB (B is non-inverting, A is inverting)
# * for UP, z=0 is IOB_xxA (A is non-inverting, B is inverting)
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