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Reconfigurable system-on-a-chip (RSoC) processors promise a low cost and rapid means of prototyping complex systems of integrated software and hardware, especially for embedded applications. Due to need to manage a wide diversity of resources on-chip, an embedded operating system is needed. We report on our experience in porting an industrial-strength embedded operating system, namely Microsoft Windows CE .NET®, on a state-of-the-art RSoC processor platform, namely the Altera Excalibur®. We report performance evaluation using a set of kernel micro-benchmarks. We also illustrate how the reconfigurable hardware resource, the programmable logic device (PLD), can be used in an application running under Windows CE.