1. Where can I learn more about combinatorial covering suites?
The doc directory contains a survey paper and a paper describing the algorithms implemented in CTS. A good introductory article about "pairwise" testing, written by Michael Bolton at DevelopSense, is also available.
3. Are the test suites produced always the same, or is there a random component in the test suite generator?
You may choose to randomize the test cases or leave them in their original, systematically-generated form. See the randomize output method for test suites and "Use Case" Number 4 in the documentation.