Interval timer problem

I do not care about the boot time of my board, and the duration of the execution of other instructions. But at a certain moment NIOS' application must produce a series of strobes with various durations. But it does not produce them because timer init instructions get stuck in layers of HAL uC. I asked how to speed up their execution. And that’s all.

It’s hard to realize this staff on FPGA logic because it works closely to other subprograms.

I got that there is no any settings in bsp property to make writing to an interrupt register exec faster.

I understand that I should work with timer like with pll. I should configure timer to produce interruptions at a fixed period, and count interruptions to produce strobes with longer duration.

Thank you.