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WiMAX promises an advanced framework to support Quality-of-Service (QoS) requirements of different types of applications and scheduling is a key part in its QoS provisioning. The scheduling algorithms used in this paper are based on our proposed Greedy-Latency scheduler, a modified form of Greedy algorithm which can guarantee delay requirements of real-time applications while optimising the system throughput. Our study of TCP performance in WiMAX shows that unlike UDP traffic, there are fluctuations in TCP throughput even for low traffic loads. It is seen that employing Automatic Repeat reQuest (ARQ) and setting the right TCP window size are crucial for a stable optimal TCP performance. WiMAX QoS mechanism can successfully maintain the inter-class priority between TCP traffic in Best Effort (BE) class and UDP in higher priority Real-Time Polling Service (rtPS) class. For intra-class scenarios, it is observed that TCP flows in general need a protection mechanism as the UDP traffic tend to seize the channel. The proposed Greedy-Scheduler can provide better intra-class protection for TCP flows due to its packet dropping policy.