Thank you for the explanation and I already knew these things, and as I said, I have no problem when working with the UNO.
It doesn't matter for the ide , if I put the Wire library folder under the /arduino/library/ folder, because it directly selects the correct wire folder according to the type of the board I'm using (avr or sam). And it chooses the correct Wire folder from the /hardware/arduino/(avr or sam)/libraries/Wire.
So this problem occures when using the 1.5.6r2 IDE, and I have to use it because I'm using the DUE board.
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.
I looked for another Keypad_I2C library which is designed for this type of use, but couldnt come up with a solution from my google hours..