Just had a quick browse through the manual. The Autopilot has what they call a "Tri-sensor" which measures water flow, salt and temperature. It sounds like based on this the system decides how much chlorine to produce. It doesn't seem to measure chlorine (I haven't heard much good anyway about fully automatic chlorinators with ORP sensors, but maybe they have improved in the meantime). The idea of the Autopilot seems to be to automatically reduce the chlorine output in cold water.
Quote from the manual:
The Tri-sensor temperature sensor works in conjunction with the chlorine % feature to automatically adjust chlorine output based upon changes in water temperature. The automatic compensation feature operates between 55°F and 125°F (13°C - 52°C). As water temperature falls below 65°F (18°C), the controller will automatically reduce the chlorine % and will reduce the maximum % that can be selected. This feature prevents the controller from generating excessive chlorine in cold water where it is not needed and prevents premature cell failure. At 55°F (13°C) or colder water temperatures, the controller will adjust to a fixed 1% output, thus preventing over-chlorination and premature cell failure.
What is your water temperature at the moment? But it sounds to me that if the system doesn't allow you to go on 100%, then you'll have to run the pump longer. And yes, if the output is below 50%, then you'll be close to 24h. Is your pump a variable speed pump? On low speed, 24 hour run time is doable. Even though I wouldn't like to be forced to run my system right on the limit.
The ideal salt level according to the manual seems to be 3000-4500ppm. You are currently at 3500, right? Maybe the system needs higher salt levels to actually get to 100%?
EDIT: Looks like you found the solution while I was typing. Give it a go...