@davetrow - I doubt you'll consider three months "soon" but the good news is version 1.2 has a feature just for you. With the plugin activated, you can go into Admin > Settings > Writing and look for Fix Existing Content. You'll find a new section for correcting the data in your database. It basically updates the database content with a version that is passed through wpautop one last time. Backup your database before you use this feature because it updates all posts and past revisions. But, it does fix the problem you experienced with the last verions.
Unfortunately when I originally read your post I didn't realize you were talking about previously written content no rendering properly. I was thinking you had problems creating new content. I had yet to use the plugin on a pre-existing site so it wasn't until last week that I realized the real problem you were referring to.
Anyway, hope you get a chance to try it out. The new features are also pretty awesome from my perspective, so in addition to better markup you'll also get a better user experience.
@cwlee - I'm pretty sure you posted elsewhere that you figured out the php code issue already, if not feel free to open a new thread and I'll keep it on my todo list for future plugins.