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As FPGA based systems including soft processors become increasingly common, we are motivated to better understand the architectural trade-offs and improve the efficiency of these systems. Previous work has demonstrated that support for multithreading in soft processors can tolerate pipeline and I/O latencies as well as improve overall system throughput-however earlier work assumes an abundance of completely independent threads to execute. In this work we show that for real workloads, in particular packet processing applications, there is a large fraction of processor cycles wasted while awaiting the synchronization of shared data structures, limiting the benefits of a multithreaded design. We address this challenge by proposing a method of scheduling threads in hardware that allows the multithreaded pipeline to be more fully utilized without significant costs in area or frequency. We evaluate our technique relative to conventional multithreading using both simulation and a real implementation on a NetFPGA board, evaluating three deep-packet inspection applications that are threaded, synchronize, and share data structures, and show that overall packet throughput can be increased by 63%, 31%, and 41% for our three applications.