Of course, but they are they same. Assuming that you mean the ISR function that works and the one that doesn't...
This one works (Arduino Uno)
// Rotary encoder interrupt service routine
volatile boolean rotating=false;
void rotEncoder(){
rotating=true; // If motion is detected in the rotary encoder, set the flag to true
}
This one does not (ATmega644).
volatile boolean rotating=false;
void rotEncoder()
{
rotating=true; // If motion is detected in the rotary encoder, set the flag to true
}