Hi Rob,
I used your MultispeedScanner 0.1.03 for Test an I2C Circuit. It works fine with a Duemilanova, but if I use an Arduino Due (with levelshifter from 3.3V to 5V) I got no Answer from any I2C chip. The change for the Due I did is to comment out the "TWBR-Statement". I used IDE 1.5.6-R2.
In this Postings you can find als some scope and small pieces from the a logic analyzer.
http://forum.arduino.cc/index.php?topic=234999.msg1692208#msg1692208
Regards, Detlef