Although the huge reconfiguration latency of the available FPGA platforms is a well-known shortcoming of the current FCCMs, little research in instruction scheduling has been undertaken to eliminate or diminish its negative influence on performance. In this paper, we introduce an instruction scheduling algorithm that minimizes the number of executed hardware reconfiguration instructions taking into account the "FPGA area placement conflicts" between the available configurations. The algorithm is based on compiler analyses and feedback-directed techniques and it can switch from hardware execution to software execution for an operation, when the reconfiguration latency could not be reduced. The algorithm has been tested for the M-JPEG encoder application and the real hardware implementations for DCT, Quantization and VLC operations. Based on simulation results, we determine that, while a simple scheduling produces a significant performance decrease, our proposed scheduling contributes for up to 16x M-JPEG encoder speedup.