The I2C bus could be on the edge of working because of too many pullup. Let's worry about that later.
The 3.3V pin on the Due is for sensors. You should use it. You should also use the GND from the Due board for the sensors.
Everything on the I2C bus should power up at the same time. If the I2C bus is already used and something is turned on after that, then the I2C bus could go wrong.
What problem are you trying to solve by using another power supply for TMP117 sensor ? It does not make sense.
Is it a very cheap DC/DC-converter ?
By the way, the I2C bus has three things: SDA, SCL and GND.