Removed index.php and getting funky URLs - using structure and nsm htaccess generator

I’ve removed index.php on dozens of EE sites without any problems, but this one is doing something funky…

I’m using NSM htaccess Generator, and Structure. The difference with this site in particular is that it was built and the entries were created before we tried to remove the index.php (every other time I’ve done it at the beginning stages of development). I’m not sure if that would have anything to do with it or not, but it is strange. (I didn’t build this one, am stepping in, so it’s a bit awkward trying to work this out).

It’s working on most every URL, except for sub-pages and category pages. I’m getting /? in segment_1 on all sub-pages and the the category id in segment_3.

Any ideas what might be going on here?

Funky URL result: http://mattgivenstudios.com/?/blog/C1/content-marketing

Here is how the URLs are being pulled, and getting the above result:

{exp:channel:categories channel="blog" show_empty="no"}        
<a href="http://{path=">{category_name}</a>    
{/exp:channel:categories}

I’ve usually used structures sub_nav tag for sub-navigation… could this possibly be an issue?

Another issue is that when I try to use strucuture’s sub_nav tag I get an error saying that tag cannot be processed…

Structure 2.2.5 is the version installed.

Any thoughts would be great, thanks in advance!