endless loop in stock interrupt handler

I have two timers:

- the timer with IRQ2 has a 1ms period (the only interrupt I see came from this timer)

- the timer with IRQ3 also has a 1ms period (surprisingly enough, I never saw this timer trigger an interrupt?)

(edit):

the IRQ2-timer is also set as the sys_clk_timer in the altera BSP editor

the interrupt handler I use in the moment, is the stock interrupt handler provided by the altera BSP:

- alt_irq_handler() in alt_irq_handler.c

here a shortened snippet from alt_irq_handler:

  active = alt_irq_pending ();
  do {
    i = 0;
    mask = 1;
    do {
      if (active & mask) { 
        alt_irq.handler(alt_irq.context); 
        break;
      }
      mask <<= 1;
      i++;
    } while (1);
    active = alt_irq_pending ();
  } while (active);
  ALT_OS_INT_EXIT();

the called handler for this particular IRQ is alt_avalon_timer_sc_irq (void* base) in alt_avalon_timer_sc.c

shortened snippet of the code:

  IOWR_ALTERA_AVALON_TIMER_STATUS (base, 0);
  IORD_ALTERA_AVALON_TIMER_CONTROL (base);
  ALT_LOG_SYS_CLK_HEARTBEAT();
  cpu_sr = alt_irq_disable_all();
  alt_tick ();
  alt_irq_enable_all(cpu_sr);

for the time being, my main() function does nothing else than controlling the blinking of an LED