In a previous paper we presented the concept, design and implementation of an FPGA run-time support system (FSS) for a dynamically reconfigurable FPGA. In this paper we discuss our experiences in running applications on the system. Problems with tool support meant that the full capability of the device could not be exploited; nevertheless, a significant application was executed under FSS control on the system. We discuss how both the application itself and the FSS were tuned to improve overall performance. The paper concludes by considering how our experience impacts upon the development of FSS-like software for the latest generation of reconfigurable devices.