cagriaksu:
My problem is with the Keypad_I2C library (I believe) because it happens to work with the Wire library for the AVR devices, but not with the Wire library for the SAM devices.
At the risk of sounding rude: No, the problem is definitely with the IDE. I looked at Wire.h and Wire.cpp for both versions of the IDE and whoever is making the changes for the SAM devices failed to maintain, or has yet to finish, the API for the Wire library. It is after all only an RC2 version. I believe RC in this case means Request for Comments so you might want to let them know on the developers list Redirecting to Google Groups.
The Wire library for the SAM devices is missing a default, or empty, constructor. You can add a default constructor but I didn't check to see if there were any other missing or modified functions in the SAM devices Wire library.