Lego open source firmware and Lejos both use 48 054 850 for 48Mhz instead of 48 000 000.
The SPI interface uses this value, so I started asking why the difference.
(too curious to just change)
Answer from the nxtasy hardware forum is it must be a multiple of the clock crystal.
The USB will not work if the value is too far off.
In AT91 datasheet p.26 states maximum limits for the crystal are listed for the USB and debugging to work.
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