I used the built-in WordPress api for custom taxonomies more throughly in the latest version which means the way the permalinks work is a bit different then what I had setup. Some users are finding that they can have both the same, but some users are finding they can't. I'm still trying to work out why this is happening.
For example, on one of my own blogs, if I have "series" in the title of any posts then I can't use
series as the custom-base for the series-toc because it will just get redirected to a post with "series" in the title (post titles take precedence over other redirects) (or I can change the slug of the posts with series in them).
I've filed this as a ticket because it's bugging me but it's not a high priority ticket as a simple name change for the series toc (using something other than series) works.
Also, don't forget that Organize Series no longer uses
series.php for the series archive pages. It now uses the new format provided by WordPress, so use
taxonomy-series.php instead. You can copy the contents of any existing series.php into taxonomy-series.php and it should work fine.