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In this paper, we study the burstification effect on the TCP synchronization and TCP congestion window mechanism. It is shown that short assembly times are optimal for flows with similar characteristics, while large assembly time provide a higher notion of fairness. In addition, this paper analyzes the synchronization of multiple TCP flows when aggregated together over the same optical bursts. It is shown that there is a strong TCP synchronization effect upon burst losses, in the sense that flows’ windows increase/decrease simultaneously, resulting to a significant variation of outgoing traffic. These deficiencies may be dealt with employing a multi-queue burst assembly scheme with different timers and taking into account the TCP dynamics.