Hi Steven I do not know the AT91SAM7S, but assume its pretty the same ADC peripheral.
No, I can not think of anything why it should not work on your S-machine. But indeed (and for historical reasons) there is another init-routine in my system - see attachment. If it works with this, then check out what you really need of it :-) Lazy approach!
Another hint: Our board runs with an external 25 MHz clock and parameters are such to bring its main clock to 48 Mhz (done in configtool).
Hope this brings you one step further. Regards Robert
ihw.c
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ihw.h
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