Issues of High Performance Computer (HPC) system diagnosis, automated system management, and resource-aware computing, are all dependent on high fidelity, system wide, persistent monitoring. Development and deployment of an effective persistent system wide monitoring service at large-scale presents a number of challenges, particularly when collecting data at the granularities needed to resolve features of interest and obtain early indication of significant events on the system. In this paper we provide experiences from our developments on and two-year deployment of our Lightweight Distributed Metric Service (LDMS) monitoring system on NCSA's 27,648 node Blue Waters system. We present monitoring related challenges and issues and their effects on the major functional components of general monitoring infrastructures and deployments: Data Sampling, Data Aggregation, Data Storage, Analysis Support, Operations, and Data Stewardship. Based on these experiences, we providerecommendations for effective development and deployment of HPC monitoring systems.