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Many sophisticated mechanisms have been implemented at both the transport and the network layers in order to estimate network conditions and avoid overload of network links. We evaluate the congestion control and avoidance scheme from a cross-layer perspective. We conduct simulations to investigate issues of miscollaboration between the network and transport layers that have negative impact on application performance. We identify several such scenarios; we discuss the reasoning and the extent of miscollaboration, and the appropriate measures to resolve the problem. We conclude that the common practise for evaluating research proposals lacks the appropriate experimental diversity, granularity or perspective and hence new mechanisms may favor a particular set of targeted protocols but damage some others. As a result, a portion of Internet traffic flows is frequently favored at the cost of co-existing traffic flows.