One thing which may help, or may not, I don't know. When you put silicone on one surface and need it to not stick against the other (as in forming a new seal or gasket) try using paste wax on the second surface. Use a light cover without any excess gobs and then wipe it when it is dry.
It sounds like you need a mold-release agent to form the gasket against one side and have it stick to the other. This works with epoxy, so I wonder if it will do the same with silicone. You might give it a try sometime. Don't know about the residual wax-developers interaction and chemistry.