The history of the application of formal methods to cryptographic protocol analysis spans nearly twenty years, and recently has been showing signs of new maturity and consolidation. A number of specialized tools have been developed, and others have effectively demonstrated that existing general-purpose tools can also be applied to these problems with good results. However, with this better understanding of the field comes new problems that strain against the limits of the existing tools. In this paper we will outline some of these new problem areas, and describe what new research needs to be done to to meet the challenges posed.