void SysTickHandler( void ) __attribute__ ((interrupt ("IRQ")));
void SysTickHandler( void )
{
s32 i;
#ifdef TIMING_ANALYSIS // to debug with a scope
// Systic flag.
GPIO_WriteBit( GPIOA, GPIO_Pin_6, Bit_RESET );
#endif
#ifdef PRIMER2
GPIO_WriteBit( GPIOA, GPIO_Pin_3, Bit_RESET ); //
#endif
....
I think second GPIO write must be inside TIMING_ANALYSIS block.