ISR is set to 1ms but still the code cant work.(every 1ms interrupt it checks on counter and operates when counter is 0. For example

void Timer2 (void) interrupt 5 using 1
{

counter--;
if (counter==0)
...
}
counter is set to 30 for each phase of stepper motor movement. So as time for the movement is 30ms and the code will still continuos check/interrupt every 1ms.

The code is sending ASCII character too. Will the interrupt affects the serial transmitting operation?
//the code is modified due to original code has no while loop