inline pull up/down resistor decrease resistance when encapsulated
It's possible the resistor is being affected, but silicone is relatively good that way compared to epoxy and 10% is a big change. 

You DEFINITELY need to avoid using acetic acid cured (condensation cure) silicone on electronics. Use an electronic grade of silicone rubber. 

Platinum-cure silicones do not have the conductive acid component.