Write "extra" in the search window and manually dust the remaining extras. Mass disenchant is taking as extra only third and all the next copies of the card AND OF THE GOLDEN CARDS. So if you have two normal and one golden, Mass disenchant did not dust the second normal one.
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Started Nov 2015 @ eu: DH 125 /Dr 268 / Hu 613 / Ma 2447 / Pa 1000 / Pr 909 / Ro 1514 / Sh 1209 / Wl 595 / Wr 538