Why is there what appears to be rust inside of the lower stainless steel chamber?

First, determine that the buildup is actually rust.  Do this by scrubbing a 50/50 mixture of water and vinegar into the problem area.  If the buildup comes out, then the buildup is just healthy minerals that the Black Berkey^® Purification Elements are designed to allow through.  If the buildup does not come out, then it is likely rust and the chamber in question should be replaced per our One Year Stainless Steel Warranty. Contact our customer service team to initiate this return.