RAMFUNC void pwm_irq_handler ( void )
{
unsigned int dummy = AT91C_BASE_PWMC->PWMC_ISR;

    //* Suppress warning variable "dummy" was set but never used
    dummy = dummy;
    
    //...
}

//...
// А вот этим запускаю прерывание, после настройки ШИМ.

AT91C_BASE_PWMC->PWMC_IER = AT91C_PWMC_CHID0;

volatile AT91S_AIC * pAIC = AT91C_BASE_AIC;
    
pAIC->AIC_SMR[AT91C_ID_PWMC] = AT91C_AIC_SRCTYPE_INT_POSITIVE_EDGE | 7;
pAIC->AIC_SVR[AT91C_ID_PWMC] = (unsigned long)pwm_irq_handler;
pAIC->AIC_IECR = (1 << AT91C_ID_PWMC);


//...

RAMFUNC void pwm_irq_handler ( void )
{
unsigned int dummy = AT91C_BASE_PWMC->PWMC_ISR;

    //* Suppress warning variable "dummy" was set but never used
    dummy = dummy;
    
    //...

    AT91F_AIC_AcknowledgeIt( AT91C_BASE_AIC ); ///> Добавил вот это
}

RAMFUNC void pwm_irq_handler ( void )
{
        unsigned int dummy = AT91C_BASE_PWMC->PWMC_ISR;
        dummy = dummy;
        AT91F_AIC_AcknowledgeIt( AT91C_BASE_AIC );
}