As Chris points out in the comments, this has been fixed now. coComment is working now with Blogger Beta popup comment forms! :D
There were things which changed when the new Beta hit, especially how third party applications worked with Blogger. I noticed this a few days back, but I thought it was just a glitch. But now, I think I can confirm that it's actually a problem, probably due to the way Blogger handles comments now (through encrypted pages).
CoComment now puts all comments made on the Beta under a Blogger: Post a comment topic, which unfortunately contains all posts made by anyone on the Beta with CoComment on. That means posts are no longer being recognised, and it's putting everything in one basket. There is the brute force way, where you have to enter all the details about the blog and the post yourself, but CoComment should be able to automatically do that. This is not good! Almost everyone used Singpolyma's excellent Comment Form and CoComment integated very nicely with it. But now, it just seems to be broken pretty badly.
I haven't tried other ways (such as the bookmarklet, or the userscript) to make CoComment catch comments and other nitty gritties posted on Blogger, but I think if this is broken, the others would be too. Do tell me if it's working for you, or behaving in a different matter than what I've seen!
C'mon CoCo! Get crackin, we need those comments chronicled!