I noticed this too, but only on certain materials. Ichor from spiders and Brimstone from the Shattered Springs were not giving double resources while using a Black Blood Pick or Eldarium Pickaxe. I had three perks in Expertise.
Which resources were you having trouble with and which tool(s) were you using?
I’ve noticed a strange thing: when I harvest stone sometimes I make 3 hits for 1 node, and larger nodes require 4 hits (I have the next perk in Expertise as well). The 3-rd hit being the last one gives twice as many resources ok, but this perk doesn’t work with larger nodes.
All resources and i was using stone tools since i just started a PvE server. I have no problems on PvP servers, the perk works just fine on all materials and resources there.