Hi Rebe,
You could try this initialisation, which assumes the 2-off ADC channels are ADC1 and ADC2. You sure you have the ADC clock right, and the source impedence of your analog stages are OK? Try putting the mcu into sleep mode during the ADC conversion.
void MCU_init(void)
{
/*** ### MC68HC908JL16_28 "Cpu" init code ... ***/
/*** PE initialization code after reset ***/
/* System clock initialization */
/* Common initialization of the write once registers */
/* CONFIG1: COPRS=0,LVID=0,SSREC=0,STOP=0,COPD=1 */
CONFIG1 = 0x01;
/* CONFIG2: IRQPUD=0,LVIT1=0,LVIT0=0,IICSEL=0,STOP_ICLKDIS=0 */
CONFIG2 = 0x00;
/* Common initialization of the write once registers */
/* Common initialization of the CPU registers */
/* PTAPUE: PTA6EN=1 */
PTAPUE |= (unsigned char)0x80;
/* ### Init_ADC init code */
/* ADCLK: ADLPC=0,ADIV1=1,ADIV0=1,ADICLK=0,MODE1=0,MODE0=1,ADLSMP=1,ACLKEN=1 */
ADCLK = 0x67;
/* ADCSC: COCO=0,AIEN=0,ADCO=0,ADCH4=0,ADCH3=0,ADCH2=0,ADCH1=0,ADCH0=0 */
ADCSC = 0x00;
/* ### */
asm CLI; /* Enable interrupts */
} /*MCU_init*/
Let the forum know how you get on...
Mark