I believe there is a paste/grease for when you rebuild wheel cylinders and they are going to sit on the shelf for years afterwards. Perhaps that would be your answer. But if you use anything that is not compatible with the brake fouid or your rubber cup, you are going to cause more problems.
I just did a google search and it looks like the product reuired is called redrubbergrease:
http://www.redrubbergrease.com/