Found a bug while setting up my new machine. I don't know the exact version of LCNC I am running but if need be I can look in the morning. I am running a 7i96 and a parallel breakout board hooked to the pc. It is 2.9 from buildbot debian stretch about a week ago.
If you tell it you have a para port and then on the page for that para port tell it that it is set for input (Pins 2-9) it ignores it when you actually write the files. It sets the pins correctly but at the beginning of the hal file I have to change it from "out" to "in". And of course because the wizard overwrites any changes I have to do it every time I rerun it. And I ran it a lot setting up homing and limits.