Nios-ll Interval Timer is not enabled

I guess the problem is that you declared this timer as system.

Let us first check the alt_timestamp_start function:

int alt_timestamp_start(void)
{
  void* base = altera_avalon_timer_ts_base;
 
  if (!altera_avalon_timer_ts_freq)
  {
    return -1;
  }
  else
  {
. . .
}

That means that you get the zero value of altera_avalon_timer_ts_freq. But why? As we can find in the altera_avalon_timer.h there is a definition for timer initialization, which is basicly looks like this:

#define ALTERA_AVALON_TIMER_INIT(name, dev) 
  if (name##_BASE == ALT_SYS_CLK_BASE)
  {
   . . .
   . . .
  else if (name##_BASE == ALT_TIMESTAMP_CLK_BASE)
  { 
    if (name##_SNAPSHOT)
    { 
      altera_avalon_timer_ts_base = (void*) name##_BASE;
      altera_avalon_timer_ts_freq = name##_FREQ;
    }
   . . .
  }

The value of altera_avalon_timer_ts_freq is getting right frequency is only when during the definition we don't have a sys_clk. Since you have it, we don't visit the else branch and we don't initialize it.

You can don't use it as a sys_clk, or create new interval timer.