Yeah, thanks Grumpy.
One thing now which I have noticed:
Originally the unit has its own power supply and is plugged in to "the mains".
Programming the Arduino meant I unplugged it and plugged the USB cable into the unit and flashed it.
Doing so, I could "test" it because the Arduino would boot.
Now with the MCP and the PULL UP resistors, nothing happens. To test the sketch I need the until fully plugged in and powered.
Bit annoying.
Is this because of the pull up resistors? Before I had them in, with the I2C bus connected at initial testing, I am sure the Arduino worked.