Most large-scale communication networks, such as the Internet, consist of interconnected administrative domains. While source (or selfish) routing, where transmission follows the least cost path for each source, may be reasonable across domains, within a subnetwork controlled by a single administrative domain, service providers often depart from selfish routing to improve operating performance. This observation suggests that the study of large-scale communication networks requires an analysis of partially optimal routing, where optimal routing within subnetworks is overlaid with selfish routing across domains. Such partially-optimal routing leads to a number of paradoxes, however. First, optimal routing within a subnetwork does not necessarily improve the performance of the overall network. In particular, we show that when partially optimal routing leads to worse overall network performance, it is because Braess' paradox can occur in the network. Second, in the absence of prices per unit of transmission, lower-layer traffic engineering within an administrative domain may prefer selfish routing to optimal routing because optimal routing typically increases the amount of flow into the subnetwork, thus increasing the delay costs.