I’m not sure how you derived those stats, but in any event 1 in 10,000 is certainly what I would call improbable. 
However, I’m more talking about Karakoth…I have done some ~200 challenges and selectively another number of PvP battles there without an arcane traitstones showing up.
To do a quick comparison, I moseyed on over to ‘Dire Straits’ in Maugrim Woods and did 20 challenges at Warlord II level:
Nil: 1
Minor: 13
Major: 4
Runic: 1
Arcane: 1 (swamp)
Celestial: 0
This is closer to a normal result, although perhaps I was lucky to get an Arcane instead of a second Runic.
Also, one of the Devs indicated there was a ‘slightly’ higher chance of getting better traitstones at a higher difficulty level. I’ll try and track down the quote and copy it here.