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I only noticed this when I attempted to modify one of my pre-existing mastery pages to use for a different champion (changed a Skarner jungler page to fit Malphite during champion select).
I only shifted a few points in the defense tree to pick up legendary armor and left Utility untouched (so always had Runic Affinity). The mastery page previously was working properly.
However, upon play, Runic Affinity no longer was in affect and both blue and red golem buffs were running out at a much faster rate. It occurred through multiple plays with this mastery page and only upon modifying it by removing Runic Affinity and reselecting and resaving the page did it seem to function as intended again.
None of my other mastery pages that i've run with Runic Affinity seems to be affected. I modified my Maokai page and shifted a mass number of points from Utility to Defense and this seemed to have no effect on whether Runic Affinity worked or not so I am unsure as to what caused this to trigger.