PRV in series with a Fixed Flow Pump
The top system in Figure 6 shows a PRV installed in series with a fixed flow pump. The bottom system shows how this system is modeled internally by PIPE-FLO. Note that the pipeline between the pump and the PRV is isolated from the tanks (this pipeline is circled in red).
BPV with a Flow Demand Downstream
The top system in Figure 7 below shows a BPV installed in a system with a flow demand set at the outlet. The bottom system shows how this system is modeled internally by PIPE-FLO. Note that the two pipelines downstream of the BPV are isolated from the tank (these pipelines are circled in red).
If parts of your system are isolated and you don't intend them to be, you should first look at the controls and the boundary conditions (pressures and flow demands) that are set in their vicinity. If your system is complex, it is often helpful to print out a FLO-Sheet and then sketch on top of each control how it is modeled internally by the program. You can then more easily see what parts of the system do not have an open path to a tank or pressure demand.