Hey! That happened to me in the last update. And from what I see on www2 and www3, Google seems to have resolved it back to the domain name without the affiliate ID. Luckily for me, Google picked it up from an affiliate who had the ID wrong - so no affiliate was getting the advantage of clicks coming in thru the SERPs.
I was asked to wait it out till the next update (this one...) andhopefully things would resolve...and I hope they have.