Interval timer problem

I don't need board to boot in less than 10 ms. My board starts for a long time. And that is all right.

I need to do something like this:https://www.alteraforum.com/forum/attachment.php?attachmentid=7682

t1 - is first strobe with a duration 10ms, t2 - time to reinit and restart timer.

To make stobe with duration 10ms I first init and start timer, and then set pioout1 up

But I can't make t2=0, because

void timer_start(void)
{
    IOWR_ALTERA_AVALON_TIMER_CONTROL(timer_base, ALTERA_AVALON_TIMER_CONTROL_STOP_MSK); //stop timer, disable interrupt
    IOWR_ALTERA_AVALON_TIMER_STATUS(timer_base, 0);                                     //clear flag
    IOWR_ALTERA_AVALON_TIMER_CONTROL(timer_base, (    ALTERA_AVALON_TIMER_CONTROL_ITO_MSK |
                                                    ALTERA_AVALON_TIMER_CONTROL_START_MSK)); //start timer, enable interrupt
    return;
}

takes 6ms!

I can set timer for 4ms it can help me get second strobe with 10ms duration, but it is dirty hack.

maybe there is some optimization, and i should turn it on in bsp/hal configuration?