Not really sure, if it is applicable in your case, but you can you try clearing the interrupt early as suggested by @richard-damon in this post:
void __attribute__((__interrupt__, auto_psv)) configTICK_INTERRUPT_HANDLER( void ){
IFS0bits.T1IF = 0;
if( xTaskIncrementTick() != pdFALSE ){
portYIELD();
}
}
Also, why do you declare vApplicationSetupTickTimerInterrupt
as weak?