Ok good it works! You said the BrickPi+ scripts weren't working? They shouldn't have said a peep about SPI, so are you sure you were runnign the BrickPi+ scripts and not the BrickPi3 scripts?
So about the firmware. The BrickPi3 uses a completely different microprocessor. So when you attempted to update the firmware for some reason it said it updated, but it actually couldn't have. I'm not sure how it checks if the update was successful or not. Anyways you did not update your BrickPi to BrickPi3 firmware. You can however update it to a firmware version that will work with your BrickPi. However you will not be able to use the Normal Update firmware GUI. It will require extra hardware.
For more info on updating the older BrickPi look here.
I would suggest though asking someone from Dexter Ind if you want to update. Not sure if the BrickPi+ firmware is compatible.