Okay, now I finally got it working. I had forgotten about the command:
After having gotten it to do readings, this command worked. So after it had programming the FPGA I rebooted just to be safe, then ran the sensors demo. It now showed zeros again. I tried rebooting again, still zeros. I tried the bash command again, but it just said it was already programmed. So I took the power from the Pi, took off the Matrix again, reconnected it again and connected the power again.
Now the readings are finally updating
So, to try and sum up the other stuff I did, I ran a git pull in every folder. I guess the most important ones would be matrix-os and matrix-creator- hal. Then I ran:
sudo apt-get update
sudo apt-get upgrade
Then did a cmake and make in the matrix-creator-hal/build folder. Then bash again:
Then pulled power from the Pi, took off the Matrix. Waited 5-10 seconds as is usually a good idea when making sure a device has lost all power, put the Matrix back in the Pi, powered on and ran
and the readings are updating. Hope this will help others save some time.