Arduino Due and ultrasonic sensor with timer interrupts

There is a great chance that you don't clear the Timer status register once the interrupt Handler has been triggered the first time. If the status register has not been read (and cleared), the interrupt handler is no more called. To debug, set a much larger interval (several ms) to trigger timerisr(), and Serial.print something to see whether you call it again or not. Of course, after debugging, you wil remove the Serial.print.

If you still have issues with the timer counter, use another one:

or make a direct register programming (numerous example sketches in the DUE sub forum).

BTW, select 250000 rather than 9600 for Serial.begin()