Both of those are much older encoders, of course (nearly 2 years old in the case of the PCS paper), and some of the settings they used were questionable, e.g., what HEVC calls "constant QP" actually varies the quantizer based on the frame type, while VP9 really uses the same quantizer, which can make a big difference on metrics. Talking to the authors at PCS, they re-ran results later with more relaxed QP settings, and VP9 got somewhat better, but still didn't catch up with HEVC (on metrics).
Keep in mind all of these results are from people who have spent significant time working in MPEG/ITU/JVT/JCTVC, and may have some inherent biases. Google's own results looked much better: http://ieeexplore.ieee.org/iel7/6729645/6737661/06737765.pdf... (sorry for the paywall, I'm not aware of a free version available online, tl/dr: 30.38% better rate than H.264, 2.49% worse than HEVC), but obviously come with their own set of biases.
I don't know how to explain the discrepancies in the two sets of results, but they at least demonstrate the magnitude of the differences you can obtain by varying how you do the testing.