The CIP system is a series of rules that describe how to assign a stereodescriptor (e.g. R/S, E/Z) to a stereocentre. When Bob Hanson decided to add support for CIP to Jmol, rather than simply read the rules and implement it according to his interpretation as others have done, he decided to work with three other implementations to challenge each other on disagreements and clarify the wording of the rules.
The result is described in:
Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. Robert M. Hanson, John W. Mayfield, Mikko J. Vainio, Andrey Yerin, Dmitry Redkin, and Sophia
Essentially, the issue that the authors are addressing is the fact that existing implementations even in "highly respected software packages" disagree with each other (see John Mayfield's presentation). By comparing the implementations in Jmol, Centres, Balloon and ChemSketch they were able to identify cases where:
"(a) the disagreement was due to different interpretations of CIP rules among software developers, (b) there was a problem with an algorithm or its implementation in code, or (c) the CIP rules themselves were flawed."
In all cases, however, they were able to come to a consensus, which led to "the discovery of a small number of errors in the Blue Book, two minor flaws in the CIP rules, and a proposal for a new rule".
The paper walks through their discussions of each rule in turn, looking at any issues arising and clarifying any ambiguities. It also includes a validation suite (browse it here) that covers all aspects of the rules and will allow future CIP implementations to avoid the pitfalls that have beset the field in the past.