I used the REG_PWM version, that works with serial!
void PWM_Handler()
{
long dummy=REG_PWM_ISR1;
.
.
}
void setupVGA()
{
pinMode(42,OUTPUT); pinMode(43,OUTPUT); // vsync=42 hsync=43
pinMode(34,OUTPUT); pinMode(35,OUTPUT); // blue (35=msb,34=lsb)
pinMode(36,OUTPUT); pinMode(37,OUTPUT); pinMode(38,OUTPUT); // green (38=msb,37,36=lsb)
pinMode(39,OUTPUT); pinMode(40,OUTPUT); pinMode(41,OUTPUT); // red (41=msb,40,39=lsb)
REG_PIOC_OWER= 0x3fc;
REG_PMC_PCER0= 1<<27;
REG_PIOA_PDR |=1<<20;
REG_PIOA_ABSR|=1<<20;
REG_PMC_PCER1= 1<<4;
REG_PWM_WPCR= 0x50574dfc;
REG_PWM_CLK= 0x00010001;
REG_PWM_DIS= 1<<2;
REG_PWM_CMR2=0x0; // REG_PWM_CMR2=0x200; //to invert hsync polarity
REG_PWM_CPRD2=2668;
REG_PWM_CDTY2=2348;
REG_PWM_SCM=0;
REG_PWM_IER1=1<<2;
REG_PWM_ENA= 1<<2;
NVIC_EnableIRQ(PWM_IRQn);
}