OK, the only change is the one from timer2 to timer1 for the Megas. That should do the trick as far as I know.
Options:
1)
We did something wrong; no idea what
2a)
Test your sensor on the Uno with boarddefs as it currently is; does it work? This will prove that your sensor is still OK.
2b)
Test your sensor on the Uno with boarddefs modified to use Timer1 instead of Timer2 (line 152/153); does it work? That basically would proof that the approach works.