Just spoke with Honeywell.
Apparently, the random 35% running time of the fan is based on a particular schedule. For instance, if heating and/or cooling has been set for the wake period, and then fan has been set to run with the system, the fan will be on 100% of the time while either heating or cooling is on. If during the wake period, the heating or cooling stops AND the conditioning period is less than 35% of total wake period, then the fan will run for up to 35% of the wake period.
This cannot be that accurate as it will require some prediction on the thermostat's part. But, I guess it can help to circulate air when the conditining part is off.
Hope this helps someone out there.