The advantage of RTR systems usually comes with some costs. The required time to map some areas of a program to an FPGA is considerable and affects the performance of RTR systems. Several methods have been developed to speed up the configuration process in these systems. Configuration compression can reduce the total number of write operations to load a configuration and it has been proven to be an efficient technique for dealing with the configuration overhead. In this paper, we have developed a new approach for reconfiguration overhead reduction in Virtex Based RTR Systems by using a compression technique based on Lempel-Ziv (LZ) algorithm. Since the order of the sequence of configuration frames affects the compression rate, we have proposed an algorithm based on Genetic Algorithm for finding the optimal configuration sequence of frames. The proposed algorithm will be applied to the input configuration file in a batch (offline) manner, and its time complexity is tolerable considering the overhead reduction obtained by having the optimal sequence of frames in run-time configuration decompression. Also, corresponding to our approach, a hardware model has been designed for configuration decompression.