The Ancient Knowledge effect given as a questreward is supposed to only affect dwarven armor, but of some reason it also boosts the defence of other set of heavy armor.

Anyone else have this problem?

Before mentioned quest:
http://www.uesp.net/wiki/Skyrim:Unfathomable_Depths

Just loaded up a save from my orc berserker character since she has that perk (currently wearing Daedric Armor) and I don't see anything like that. Are you sure it's not just the skill increasing or an enchant/another perk of some sort?

Ya I just did this quest a cpl days ago and noticed what the ancient knowledge did yesterday. I switched to heavy armor yesterday(dragonbone) and it hasn't effected my dragonbone armor.

Are you sure? Did you calculate your armorrating? ( http://www.uesp.net/wiki/Skyrim:Armor )

As far as i know, it is still bugged and work with all armor. The "Blacksmithing increases 15% faster" is also not fixed and give a steady 15 (hidden) points to smithing instead of a faster skill increase.

That's my understanding (and experience) too. I think their confusion comes from not noticing a diff between heavy and light armor (or types), which is precisely what you'd expect due to the bug giving the bonus to all armor types. (Personally, I kind of like the bug as it makes the quest useful to every armor-wearing character build.)