Interval timer problem

How do you measure the strobe ? You power up the board and start a chronometer until your "err=1" happens ?

uC/OS has its own initialization that shall take time.

Do you want your board to start very fast ? Why such a constraint.

OR do you want your board to "produce" a regular strobe ? which is more usual. I think you want THIS.

You code is hard to understand.

static void handle_timer(void* context)
{
    IOWR_ALTERA_AVALON_TIMER_CONTROL(timer_base, ALTERA_AVALON_TIMER_CONTROL_STOP_MSK); //disable interrupt
    IOWR_ALTERA_AVALON_TIMER_STATUS(timer_base, 0); //clear flag
    IOWR_ALTERA_AVALON_PIO_DATA(PIO_BASE, 1); // <----------------------This is THE stobe signal, I think
    timer_exit(); // <--------------------- ?????????? ----------------- you are in an interrupt routine, so it should be as short as possible and easy to read
    err = 1;
    return;
}

Your code doesn't do what you expect (I am 95% sure). I suggest to rewrite the code.

Keep in mind the algorithm of what you expect.

Regards