The window that the IDE shows when you click on Peripherals -> Analog/Digital Converter doesn't seem to control the checkboxes properly for the Channel Status register bits ADC_CHSR[7:0]. I'm using an ATMEL AT91SAM7S32, and in my ADC init function I write 0xFF to the ADC_CHSR register, which should enable all 8 A/D channels to be A/D inputs. But... only the checkboxes in the ADC window associated with ADC_CHSR[3:0] get checked. I changed the code to:
ADC_CHSR = 1 << 0; ADC_CHSR = 1 << 1; ADC_CHSR = 1 << 2; ADC_CHSR = 1 << 3; ADC_CHSR = 1 << 4; ADC_CHSR = 1 << 5; ADC_CHSR = 1 << 6; ADC_CHSR = 1 << 7;