If I look at the pulse signal being sent to the step driver and also look at a test signal (A3) that I set high at the start of the ISR for the buzzer and low at the end of it, I can see that when this interrupt fires it also interrupts the pulses being sent by the other interrupt and changes the width of the pulses, leaving it high or low for a longer period than it should be therefore making a clunking sound.
I have attached both the source and header files for the Timer1 and Timer3 libraries. Also here is the link to the webpage - Arduino Timer Lib Page
My motor seems to run perfectly if I don't another interrupt.
TimerOne.cpp (7.83 KB)
TimerOne.h (2.94 KB)
TimerThree.cpp (4.1 KB)
TimerThree.h (1.31 KB)