I inverted the limit switch pins in io.hal. I also added the estop input as I noticed it was missed completely. Even after adding it doesn't function, although I can see the estop signal change when I push the physical switch.
I added the external estop input code just now and added the invert a few days ago so get a fresh copy of the deb and you should be good to go. Just to be safe rename the configuration after you open it with the 7i96 Configuration Tool then build after selecting the estop input.