I'm out of ideas.
Basically, if you measure actual voltage using a voltmeter, and log voltage in the scanner, and those two match all the time, then the voltage signal from the LC-1 (or sensor itself) is suspect.
If the measured voltage and logged voltage don't match at the same moment in time, then the EIO box is suspect. Especially if the logged voltage is primarily 0 or 5 the majority of the time, and the actual voltage is not 0 or 5...