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Errors due to imperfect boundary conditions in numerical relativity simulations of binary black holes can produce unphysical reflections of gravitational waves which compromise the accuracy of waveform predictions, especially for subdominant modes. A system of higher order absorbing boundary conditions which greatly reduces this problem was introduced in earlier work [arXiv:gr-qc/0608051]. In this paper, we devise two new implementations of this boundary condition system in the Spectral Einstein Code (SpEC), and test them in both linear multipolar gravitational wave and inspiralling mass ratio 7:1 binary black hole simulations. One of our implementations in particular is shown to be extremely robust and to produce accuracy superior to the standard freezing-Psi_0 boundary condition usually used by SpEC., Comment: 24 pages, 11 figures (Figs. 9 and 11 showing CCE and extrapolation results are new), accepted by Classical and Quantum Gravity