Just released Manga+Press 2.9.1, which addresses the MIA comic problem that some users have reported. You can download the new version on WordPress.org.
A bug came to my attention recently and I’m currently in the process of working on a fix. Anyway, 2.9 introduced some interesting things behind the scenes involving the Series taxonomy. Essentially, with 2.9, you need to have a comic assigned to a Series category in order for that comic to be displayed properly. I’ve gotten two reports of comics throwing 404s and/or navigation not displaying correctly. After much effort in attempting to reproduce the issue, I found that when you create a comic post without assigning a series cat directly following installation, you will likely experience this error. However, if you go back to the comic in the WP admin and attempt to assign a category, it should still work and you should be able to see your comic.
That’s it for now. Will keep the blog updated as needed.