I had this experience when Atmas were introduced. Yes, I had zenith relic equipped (had all zeniths at the time), and ran around for months without a single atma drop. That was the time I gave up on relics past zenith, because I refused to waste months of my little playing time on something that almost never drops.
Then, came the increased drop rates, and I decided to give it a try. Got all 12 atmas in about 4 hours, 3 times already (for Thyrus, Curtana/Holy Shield, and now Sphairai). Drop rates are now more sane.
So, check the obvious above:
- Do you have zenith sword and shield equipped?
- Did you complete the quest "Up in Arms"? (check your journal under completed quests - sidequests)
- If you have completed it, Jalzahn (North Shroud 30,19, near Gerolt) should have a red quest icon.
I haven't heard about the bug you reported, but I would check if you have the conditions set for atmas dropping.