The successful deployment of low-power wireless sensor networks (WSNs) in real application environments is a much broader exercise than just the simple instrumentation of the intended monitoring site. Many problems, from node malfunctions to connectivity issues, may arise during commissioning of these networks. These need to be corrected on the spot, often within limited time, to avoid undesired delays in commissioning and yet a fully functional system does not guarantee that no new problems will occur after leaving the site. In this paper we present the first ever (to our knowledge) implementation of a handheld diagnostic system for fast on-site commissioning of low-power IPv6 (6LoWPAN) WSNs as well as troubleshooting of network problems during and after deployment. This system can be used where traditional solutions are insufficient to ascertain the root causes of any problems encountered at no additional complexity in the implementation of the WSN. The embedded diagnosis capability in our system is based on a lightweight decision tree that distills the functioning of communication protocols in use by the network, with a major focus on interoperable IPv6 standards and protocols for low-power WSNs. To show the applicability of our system, we present a set of experiments based on results from a real deployment in a large construction site. Through these experiments, important performance insights are gained that can be used as guidelines for improvement of operation and maintenance of 6LoWPAN networks.