Arduino Mega not all interrupt pins working (solved)

Posting code fragments will might get you guesses, not answers. You cannot test compile or test fragments.

Here's my guess.

void count1()//ISR
{
  //set=true;
  static int8_t lookup_table[] = {0, -1, 1, 0, 1, 0, 0, -1, -1, 0, 0, 1, 0, 1, -1, 0};
  static uint8_t enc_val1 = 0;
  enc_val1 = enc_val1 << 2;
  enc_val1 = enc_val1 | (PIND & 0b11) ;
  enc_count1 = enc_count1 + lookup_table[enc_val1 & 0b1111];
  
}