I've found out that, Wire library is located under two folders in 1.5.6r2
one for avr devices,
/arduinoIDE/hardware/arduino/avr/libraries/wire/
and for sam devices;
/arduinoIDE/hardware/arduino/sam/libraries/wire/
Their contents differs from each other, thats why when I select the board as UNO or MEGA it compiles the code, because it uses the old Wire library which I was using in the IDE 1.0. But when I select the DUE board, it switches to the new Library which doesnt seem to support the functions that Keypad_I2C is requesting for.
On the version 1, I've downloaded the Wire library from the playground and manually put it under /arduinoIDE/libraries/Wire
I'm running linux by the way