Hi ajayver... I'm having multiple issues with your plugin and I'm wondering if using "pretty permalinks" is the issue. Sorry about the long explanation...
Our base url permalink string is "ncdd.org/rc/item". The logic to this naming convention is that each blog post is an "item" in a resource center.
So manually typing "ncdd.org/rc/item/tag/tag-name" generates the proper list of posts and paginates correctly.
So does, "ncdd.org/rc/item/category/category-name".
When using the plugin and only choosing a category it generates "ncdd.org/rc/category/category-name" which sends a user to a 404 page, note the missing "/item".
Strangely though, the plugin generates "ncdd.org/rc/category/category-name/tag/tag-name" (with no "/item") when choosing both a category and a tag and this works on page one. However, pagination, adding "/page/2" to the end of the url, sends the user to a 404 page.
Manually adding "/item" to the above, "ncdd.org/rc/item/category/category-name/tag/tag-name", also sends a user to a 404 page.
I realize that removing the "/item" in the custom permalink might correct the issue. Unfortunately, we have too many absolute links that use the "/rc/item" structure on our site and on other sites to make that a reasonable solution. Also, it wouldn't necessarily have any impact on the pagination addition leading to the 404.
I'm using the latest version, have refreshed and revisited my blogs rewrite rules and even tweaked your code a little thinking it was an issue with adding the "/item" element of the custom permalink. But this behavior doesn't change.
Can you give me your thoughts on this?