Hi Michael
As I'm not a geologist or owt, I can't offer any expert advice, but have been thinking about this a fair bit recently...
I was trying to dig out a nice photo for the monthly wallpaper over at the Heritage Action website (http://www.heritageaction.org) when I came across our photos of Bryn Celli Ddu - I remembered a discussion on this from last year and lo and behold, some photos of the very stone in my collection!
I was unaware of the discussion on my visit, and only discovered it afterwards. Looking at the photos though, and with the benefit of hindsight, I'm absolutely convinced you're right on this one! It looks exactly like a tree trunk. Astonishing, as you say, that nobody's picked up on it previously!
Hopefully one of our resident geologists will be able to shed some more "official" light on this, cos it'd be great to know for sure :)
G x