For the 10-show-existing-frame, the source file indeed has a timestamp of 3 (or 100/33) for the second visible frame, so the fix appears to work correctly. For the other, only the timebase is fixed, but again appears to be correct now.
The fate results change because we now correctly timestamp the pskip frames, which means the results are now identical to -vsync 0.
Sample available at: http://downloads.webmproject.org/test_data/libvpx/vp90-2-16-intra-only.webm