Reason for this is that dev`s thought in 50 lvls you should develop all skills you wanted, and in game found enough runes for that too.
So after 50th lvl you get 50% runes for secondary skills, just for fun of it.
There is easy way to change this, but i think it will work only for new game, not one already started. If want it ask, i`ll explain.
Also if you want runes, there is always cheat for it.
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